The scope of this question runs from 1866 with the defeat of the Austrians in the Austro-Prussian war of the same year through to the split of Germany in 1945 after Hitler's defeat.

As a side note before I begin, the 'little' German nations, such as Hanover, Saxony, and Bavaria were not inconsiderable nations in their own rights. That Prussia, through the will of Bismark, was able to unify them under one flag was due in part to a nationalist zeal ignited in the post-Napoleonic period, and also in part to the declining influence of Austria/Austria-Hungary in the corresponding period. There was a desire by the rulers of the smaller constituent parts of the Germanies to avoid outright conquest by Prussia, as well as a desire to enact social reforms without a revolutionary bloodbath that had swept up France in 1792. The 1830 and 1848 revolutions stoked German liberalism and nationalism, and it took all of Bismark's political acumen to convince the disparate German nation states that the Prussian constitution and military might were worth binding under, vis-a-vie Austrian hegemony (which is why the Prussians fought the Austrian-Prussian war).

Prussian desire for hegemony arose after the 1815 Vienna settlement in part because Prussia feared Austrian, French, and Russian encirclement. The treaty had two outcomes that would shape the rest of 19th century German history: 1) The establishment of the German Confederation, made up of 39 independent states, and 2) the treaty had ceded territory on the Rhine to Prussia. This had put Prussia under considerable internal strain, as geographically, culturally, and politically the west of the new nation was far removed from the Berlin Prussian monarchy. Napoleon's sparking of nascent German nationalism during his conquest of the Rhineland was fanned by the liberalisation of Europe during the period 1820-1848, which the Austrians under Metternich attempted to suppress. Prussia was kept in check by Austrian military and political supremacy during this period, but as Austria lost political prestige Prussia began to reassert herself, especially when Otto von Bismark became Prussian Chancellor in 1862. Prussia, with the suport and aid of Austria, fought the 1864 Second Schleswig war against Denmark, which gave them control Schleswig-Holstein. Prussia then went to war with the German Confederation, led by Austria, in 1866, with led to the defeat of the Confederation and then to it dissolving as a political entity. in 1867 the Prussians unified the northern german states into the North German Confederation, which had a federal constitution with Prussian monarch as the head of state.

The German empire was formally declared at the Palace of Versailles on 18th January 1871, at which point the independent principalities and kingdoms of the North German Confederation, led by Prussia, merged with the south German kingdoms and principalities. At this point the various independent entities that had formally been part of the Germanies became states within the new German Reich, with their own laws, customs, and state legislatures. Central authority in the empire rested with the Emperor and the Reichtag, though the democracy that Bismark, the Prussian prime minister, envisaged was of a limited form, with ultimate power resting in the hands of the German Kaiser, who was also the King of Prussia.

Initially the 27 constituent states that formed the newly unified Germany were left to manage their own internal affairs without too much interference from Berlin, as Bismark did not wish to empower the Reichtag with too much power. Over the course of the period between 1871 and 1900 the German state centralised federal control in the hands of the civil service through the State Secretaries, with the effect that even though there was near-universal suffrage in Germany for most adult males, the power of their elected representatives was muted when compared to the bureaucrats who controlled the affairs of state at the behest of the Kaiser.

The effect for the 27 state rulers was that their pre-1871 powers were constrained by the 1871 German constitution. All states sent deputies to the the upper house called the Bundesrat, and although all states were nominally equal in the eyes of the law, as Prussia was the largest state in terms of both population and size they had 17 of the 58 seats, which meant they had little difficulty in obtaining the majority they needed to pass favourable legislation.

One key area the 27 states maintained their own control was the armed forces, so that the larger states, such as Prussia and Saxony, had their own armies, which in turn was modelled on the Prussian army. This had the consequence that during WW1 many regiments were led, or had a titular head, by members of the royal families from the various states.

In terms of the pre-1871 monarchs, Saxony's monarch Fredrick Augustus III abdicated in 1918, turning Saxony into a free state in the Wiemar republic; the same happened with Bavaria, and by the declaration of the armistice on 11th November 1918 all the monarchs who remained in power after 1871 had been removed from power in favour of republican ideals. The reasons for the loss of power are varied, ranging from a general disdain for support of Prussian policies during WWI (in the case of Bavaria and Saxony), to a ground-swell of desire to reform the country after the catastrophic defeat caused by the allies. The monarchical principals of power were discredited in the eyes of the German public by the actions of the ruling elite during the war, even to the point where the Bavarian's sought a separate peace with the allies.

Dues to this, many royal titles were abrogated in 1918, with all temporal power being transferred into the hands the people. The Wiemar government did not removed smaller titles, though, and those landowners, including the Prussian Junker class, were still classed as nobility through the Wiemar and Nazi governments. The fall of Germany in 1945 resulted in a complete overhauling of the governance of Germany in the East and West, with the nobility loosing all their privileges in the process. It is also worth remembering that many of the Prussian noble houses were absorbed into present day Poland and the Baltic states, were their estates were seized by the Communists and turned over to state control.

So, in summation to your question: Most of the German monarchs, Dukes, and princelings of the pre-1871 era were allowed to remain as heads of state of their respective German state (much like a US governor). Due to the actions of the various monarchies during WW1 when the German Republic was declared in 1918 the states transitioned from monarchies and hereditary rulers to directly elected state legislatures, and the former monarchs either went into exile or were settled into civilian life.

If you would like to read further, please check out the books below.

Source material:

'The Pursuit of Power: Europe 1815-1914' by Richard Evans

'The Army of the German Empire 1870-1888' by Albert Seaton

'Contesting the German Empire 1871 – 1918' by Matthew Jefferies

*Edits tidying up grammar, punctuation, and readability

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The change from lots of independent states to a single German Empire wasn't as drastic as we often assume; historically, these places had all been part of the Holy Roman Empire and the struggles between centralised Imperial v Local power had been ongoing through much of the middle ages, exacerbated by the appearance of a religious divide during the 16th century which culminated in the 30 years war.

Even after the defeats of Prussia and Austria by Napoleon and the dissolution of the HRE, there was a recognition that some form of supranational organisation would be in everyone's best interest - the Zollverein (Customs Union) was formed in 1834 and the Norddeutscher Bund (North German Confederation) in 1867. While both of these were pushed forward by Prussia (particularly under Bismarck as Prussian foreign minister after 1862 and North German chancellor after 1867), there was a growing pan-Germanism in popular sentiment too, which came to a head in the revolutions of 1848 and took much of its imagery from the perception, partially true, that Germans from different states had banded together to fight Napoleon - particularly after in 1840 the French PM Adolphe Thiers had claimed that the Rhine was the "Natural Eastern Border" of France, triggering the Rhine Crisis and sparking what was known as the "Rhine Romanticism" of the 1840s in Germany exemplified by songs such as Die Wacht Am Rhein (Watch On The Rhine) and of course the Deutschlandlied, the national anthem in various forms since 1922, written in 1841.

So the idea of a united Germany was not a completely new one by the time of unification and Prussia under Bismarck had used wars against Denmark (1864) and Austria (1866) to build national feeling and establish Prussia as "Top German".

So, to address the question directly - the unification of 1871 took in four kings: Prussia, Bavaria, Saxony and Wurttemberg, as well as a number of Grand Duchies, Duchies and Principalities as well as the three independent Hanseatic City States of Hamburg, Bremen and Lubeck - 26 in all. In fact, legally the German Empire was simply a renaming of the North German Federation to reflect the fact that it now included South German states such as Bavaria and Wurttemberg.

The structure of the German Empire as proclaimed was that of a Federation of Rulers, with the German parliament composed of representatives from all of the states, and the title given to Wilhelm I of Deutscher Kaiser ("German Emperor") was specifically chosen by Bismarck to placate the other Kings who objected to the formulation Kaiser von Deutschland ("Emperor of Germany") - it seems like a minor distinction, but the former admits the albeit theoretical possibility of other Emperors in Germany - much in the same way as after her divorce "Princess Diana" became "Diana, Princess of Wales".

So the short answer is that nothing happened to the other rulers exactly - they kept their titles and palaces, their rights and status. Actual power now rested with the Kaiser and the German Parliament (and with proportional representation for the states, the representatives of massive, populous Prussia could outvote pretty much any other combination), so depending on the ruler they may have had less real power. One concession that was made by Prussia was that the four kingdoms would each retain their own independent armies, with their own uniforms, awards and organisation, but subject to an Imperial foreign policy - in the end the smaller Wurttemberg army decided to integrate into Prussian forces. Gradually the various armies harmonised their uniforms and equipment on practical grounds but in 1914 the Royal Bavarian Army (for example) was still at least theoretically an independent force of over 80,000 men under the command of the Bavarian Crown Prince Rupprecht.

Some of these rulers lost their positions, land, even lives, during the chaos that overwhelmed Germany in 1919-21, but several of the smaller ones particularly remained in (now largely honorary) positions until the Third Reich.

Margaret Wightman, The Faces of Germany

Kurt F. Reinhardt, Germany: 2000 Years

Deutsche Bundestag, Fragen an die deutsche Geschichte

Philip J Haythornthwaite, World War One Source Book

There may or may not be a slightly wrong assumption in the question (all their little Germanies). While it's true that there were more than a thousand states in the HRE at some point, this wasn't the situation anymore in 1871.

So, what happened? The French Revolution. When the revolution successfully counterattacked in 1792, they occupied the territory west of the Rhine ("links-rheinisch") and pooled the territories into one state, the République cisrhénane.

Napoléon annexed that territory to France, and forced the HRE to accept that. That lead to the situation that the HRE had to compensate the princes that lost their territories there. So the greater states of the HRE counseled in a Reichsdeputation how to handle this. There results were revolutionary.

The Reichsdeputationshauptschluss provided the grounds for the expropriation of most of the smaller territories. The ecclesiastical states were secularized. The greater states used the situation to extend their territory ruthlessly.But also some small states used the situation; Baden for example grew three times in size.

In 1806, Napoléon forced the smaller states of Germany into the Rheinbund, which contained all of Germany without Lower Saxony (which was annexed by France), Prussia and Austria. It consisted of 23 members in 1808.

After the fall of Napoléon, the Deutscher Bund was formed. It contained the later German Reich plus Austria, Luxemburg and Liechtenstein (but lacked Elsaß-Lothringen of course). It had 39 members in 1820.

In the 1848 and 1866 wars, Prussia annexed some territories (and bought some; Lauenburg), for example the kingdom Hannover was made a Prussian province.

So when the Unification came around in 1871, there were only 26 states left.

Of these, four were Kingdoms.

The King of Prussia became also the German Emperor, as we know.

The King of Württemberg, Karl, privately supported the Unification, but had to fight against Prussia in 1866. He largely retreated into private life after 1866, which lead to the situation that his ministers could more or less do what they wanted.

The King of Saxony, Johann, supported a Großdeutsche Lösung and allied with Austria. He lost on its side in 1866, but was appeased by Bismarck's guarantees of the survival of Saxony as a state (oppossed to annexation by the Prussians, a thing which, btw, Fredrick the Great describes in his Politisches Testament as a goal for Prussian politics).

The King of Bavaria, Ludwig II. was dismayed by his failure to defend Bavarian independence, and contemplated suicide in 1867. He sent his brother, the unfortunate Otto, to be present at Versailles. A notable loner, Ludwig increasingly withdraw from politics even more. This lead to the same situation like in Württemberg, that the ministers largely could do what their thing; their thing was declaring him unfit to rule in 1886.

As to the authorities of the monarchs of the states in the German Reich:

The monarchs of the states had diverging responsibilities, the states in the Reich continued the constitutions pre Unification. But most of them were constitutional monarchies in varying degrees anyway.

Sources: Mann, Golo: Deutsche Geschichte Craig, Gordon: Deutsche Geschichte