There have been other eras that people will argue about--whether it was the seeds of the Shi'a vs. Sunni conflict, or when it really become permanent in the wake of 1501 when Shah Ismail took over Safavid Empire and really created the Sunni/Shi'a split we see today. See here for more on those two, especially in the second comment (okay, people can make a pretty good argument that the Sunni/Shi'a the wake of the Safavid takeover of Iran is pretty good "Reformation" that radically reshaped the Islamic world--from Indonesia to Islamabad to Aleppo, we're seeing fights based on that).

However, I think the best argument is that we're undergoing one today, at least in the Sunni world. Salafism is explicitly a reform movement within Islam. They want to bring back Islam to the purity of the Salaf (the first few generations after Muhammed), which is actually quite similar to the Protestants' claim that they are restoring the original Apostolic Church after its "Babylonian Captivity" in Rome. Though Salafism has in name been around for a while, it really started to take off only more recently. It's very influential on the Arab side of the Persian Gulf, where outsiders generally call it "Wahhabism" (though insiders just refer to it as Wahhabism). We can probably trace our present Salafism more or less to al-Wahhab (1703-1792), though it's a more diverse movement than just one man.

While most violent Jihadists today are Salafi influenced, and Al Qaeda and ISIS definitely are, most Salafists aren't Jihadists. There are a wide range of quietest Salafists, for example, the al Nour party which got ~25% of the vote in the last Egyptian Election. Also, a lot of the people who support Salafist Jihad are not themselves Salafists (see the excellent "Radical Sheikh" chapter in Charles Kurzman's Missing Martyrs about this--it's a "Che Guevara" like effect, where most of the people who "support" radical violent revolutionary communists like Che actually support his resisting "imperialism" rather than his stated goals of creating Communist states). An important thing to note, though, is that most Salafis don't believe non-Salafis aren't real Muslims, they just believe they are bad Muslims--that said, some do (especially Shi'a Muslims, as we have seen with ISIS) and engage in what's called "takfir", which means declaring Muslims to be kuffar (unbelievers) and therefore able to licitly killed. Again, that's a minority. Salafis from the Gulf spend more money sending out peaceful emissaries to other Sunni majority countries (which has made a lot of these countries much more conservative--not long ago, I read an interesting article about this happening the Maldives to give one example) than they do sending guns to ISIS or Al Qaeda, but however you want to put it, the Salafi movement(s) have been hugely influential to contemporary Islam and will continue to be into the future.

However, as we saw the Reformation (which split Protestantism off from Catholicism) went hand-in-hand with the Counter-Reformation (which inalterably transformed the Catholic church and made it much more formal and engaged with the laity), so too has the Salafi movement influenced a much broader movement of "Liberal Islam". That's not a name that the vast majority would ever use for themselves, but they don't have a real name. I am using Liberal Islam because of Charles Kurzman source book of the same name (take a look at the table of contents to get a picture of its scope) (Kurzman started his career writing about the Iranian Revolution so his book contains both Sunni and Shi'a sources). And they are also not merely a reaction to the Salafis, but a movement that has existed independently for a long time (again as a loose parallel, some ideas that become important to the Counter-Reformation had been around for centuries before the Reformation). The labeling of these various streams as a united movement is also relatively new, though many can be nominally traced back ed to al Afghani, or well, if not him directly, circumstances and realizations similar to his. I am currently trying to finish Kurzman's book the Missing Martyrs (which I picked up forever ago), and he makes a passing reference to the fact that in 1990, most of these "liberal thinkers" only knew other thinkers in their native countries, but by 2000 this all had changed and there are increasing ties from Morocco to Indonesia (the traditional antipodes of the Muslim World, but obviously also in the Muslim diaspora in Europe and North America). These non-Salafi international ties are very new and it's hard to see what they will become. It's hard to see exactly how much they influence each other because modern Islamic scholarship doesn't really have a norm to cite each other, but these works are ever more widely available in translation in Arabic, Turkish, Urdu, Indonesian, etc. and these scholars meet at ever more international conferences. These liberal Islam thinkers are far different from the secularists from Muslim majority countries (Ataturk, Bourguiba, Nasser, Sukarno, etc.) who were often hostile to religion, or at least treated it like a folk custom of the masses (and also different from their successors who would sometimes use religion more fluently). The political side of this liberal Islam is generally influences by the Muslim Brotherhood, which was founded in 1928 and had a brief flirtation with Jihadism in the 1960's when Sayyid Qutb was influential, but the mainstream firmly rejected with works like Preachers not Judges. The lines are definitely not as clear as the Protestant Reformation, in large part because there is no single authority structure like the papacy to enforce a sort of orthodoxy. We're talking not just two groups but many that are in conversation with each other, but suffice to say, there are a lot of changes going on during what's sometimes called "the contemporary Islamic/Muslim Revival". Again, though, like the Salafis, not all the "Liberal Islam" groups are political. It's also worth remembering that in 16th century, when you had the Papacy, you had humanists on the fence like Erasmus, you had the Lutherans, you had the Calvinists (who the Lutherans didn't always cooperate with), and then you had a lot of separate groups that scholars today often group together under the heading "the Radical Reformation" (pacifist Anabaptists like the Mennonites and Amish; violent Anaptists like those that took over Muenster; the Hutterites; various Unitarian Groups like the Polish Brethren; etc.). Today, we have a lot of different groups and it's unclear how exactly they will all be classed in 100 years. There's a decent chapter on this issue in the Missing Martyrs ("Liberal Islam versus Revolutionary Islamism"), and there are various books about small aspects of what's going on, like Saba Mahmood's Politics of Piety: The Islamic Revival and the Feminist Subject, which covers a lot of the more conservative but not necessarily Salafi Islamic revival in Egypt, and Amira Mittermaier's Dreams That Matter: Egyptian Landscapes of the Imagination which covers a similar space, but looks at religious revival in much more liberal publics (for the record, I found both books almost unreadable because of their writing styles). I don't know of any single book or article that really looks at the issues globally, and I am not sure one could write one just because the issues involved are changing and unsettled and the lines separating groups and affinities uniting them are blurry in many cases, even at the top level and definitely at the popular level. I tend to study the political side rather than the theological side, so maybe there is a better book than Kurzman's (i.e. not just a sourcebook but analysis) for some of the theological things that are happening now.

Apart from the Shia/Sunni split the closest would be the rise of Wahhabism during the 18th century though of course it didn't have as great a political competent until after WW1 and the collapse of the ottoman empire. Its could be possible to argue that the 20/21st century power struggles of the gulf states are very similar to the wars of the reformation in overall goals if not strategy.

In truth some of the fundamentals of both Wahhabism and early Protestantism are very similar, concentrate on the holy text itself and removing impurity of worship (for the protestants this meant whitewashing churches for Wahhabi this meant removing the magicians and the worship of saints). This of course is a massive oversimplification but its a useful compression between the two.

Islam used to be a lot more diverse in the past. What many people today think is "real" Islam is actually many times a very modern interpreation.

Today most Muslims believe that the Koran is eternal, however in the 8th to 10th centuries the prevalent view was that the Koran was created. This has to do with Mutazilites. Within Sunni Islam at that time there was a big fight between two main philosophical interpretations of Islam, the Mutazilites and Asharites, with the Asharites winning and becoming the dominant interpretation. This later led to the closing of the doors to "ijtihad".

http://en.wikipedia.org/wiki/Mu%60tazila

http://en.wikipedia.org/wiki/Ijtihad

No upheavals or reforms but like most religious scripture, its' interpretation has been molded to fit the ambiance of differing eras.