Archaeologist here:

For the Medieval Period we are lucky to have several more or less preserved boots and shoes, found in excavated graves, trash pits and (the best ones) from swamp deposits.

The simpliest way to describe a medieval shoe is to say that it was a leather sock, with a sole of harder leather sewn in, and then the boot/shoe was turned inside-out (they were soft enough to do that easily), so the stiches were on the inside. Then, the shoe was often smeared with hot beeswax to make it partially waterproof, and seal the stiches.

This kind of shoes were surprisingly comfortable, albeit quite soft. The results from modern reconstructions (experimental archeology) show that this kinds of shoes were very comfortable when used on natural terrain, but one would have to be careful not to step on sharp rocks (this was rather to prevent the sole from being damaged, than any discomfort to the foot). Other than that, soft, leather-soled medieval shoes provide very good traction on uneven terrain, allow one to climb, ride a horse without stirrups, dance and fight comfortably. However, they are quite uncomfortable on very flat hard surfaces like concrete, marble floors, flat cobblestones or modern sidewalk plates, which might be a clue why this kind of shoes were not worn in the modern, urbanised era.

People would wear said shoes all the time, including indoors, but when working around the yard or within a township, they would often wear special large slippers over the shoes (imagine a very large slipper woven out of hay, straw, birchbark or softened reeds). This was to prevent shoes from being soaked in muck and mud.

There seem to not have been anything resembling shoe-sizes: the shoe/boot could be wrapped or strung looser or tightier depending on the wearer, especially since it was often worn over a thick woolen sock, or linen foot-wrappings.

These are examples of reconstructed medieval shoes from Birka (Sweden), and Coppergate

http://stolte.files.wordpress.com/2010/09/img_4288.jpg (long boots)

http://boran.freehost.pl/buty/jorv1.jpg ("Jorvik shoes" with iceskates made of bone)

Sources:

A. Kovalska, Miedieval shoes of Wolin

M. Sangarov, the history of shoes

In China many shoes were made with layers of starched cloth darned together as sole. They can be as thin as normal flat shoes or several inches thick worn by upper class. The more exaggerated versions are still worn by traditional opera singers as part of their costume (not only they give the wearer a slow but steady gait, they also distinguish the authoritarian male roles from female or lower class male roles as all performers were men back in the day).

Here are two examples of handmade upperclass women's shoes from 1800's. The top pair was worn by Han women with bounded feet (common after Song Dynasty) and the bottom pair was worn by Manchu women with unbounded feet. The platform can be made from layers of starched cloth or simply carved from wood and covered in cloth. According to the sign the height of the platform grew taller and taller over the years (these are worn by Empress Cixi, they are at least 4 inches tall). The platform shoes forced the wearer to imitate the gait of Han women with bounded feet. Not all shoes were that tall though, thinner soles were also common.

Going back further shoes with raised head were popular in the Tang Dynasty. Not a lot of actual examples survived but here are some examples of ceramic or metal figurines from that time: men's shoes, men's boots, Emperor's shoes, Lady's "Phoenix head" shoes.

Wooden shoes similar to geta were also worn in the rain or mud. Example one and two.

First of all a little clarification: "These men were not professional soldiers, but farmers and such who were recruited to fight wars ad-hoc." Not exactly true, don't forget mercenaries and the fact that there were men who were prepared to fight in a war, since they were recruited regularly by their lord (knight).

Now, on the topic of boots, I can speak for late XIV/early XV C and the Viking era. This is what a knight would wear on horseback. If you unfold them fully, they reach to your thighs to avoid sores from the saddle. They're pretty comfy, except you have to stretch them first to better fit your leg which results in a few days of pain. More for everyday use, these. There were some higher ones as well, often worn by soldiers. They're generally really ok, except for the lack of friction, their sole is smooth. Makes it easy to slip.

Same goes for viking shoes. That's only one of many examples. If well made, medieval boots/shoes were really comfortable.

Fun fact: sometimes, in later medieval, people would not wear shoes, but have their leggings made with feet (like feetie pyjamas) and sew in a leather sole. Cheaper than full shoes and saves you the effort of putting them on.

This is a fascinating field called experimental archaeology. In addition to Hygrocybe's post, you could always purchase some replica shoes and try them out for yourself!

18th Century - while not asked for it may be of interest. I am not a historian, but a historic reenactor. I can tell you from personal experience how replicas are to walk in for a long day.

I will discuss the low heeled shoes worn by both men and women in this general time frame. Commonly they had buckle (or sometimes ribbon) closures. Historically they were construed straight lasted. This means that there was no difference in shape between the right and left shoes. Shoes were made of leather, and in some cases were covered in silks and satins. Heavy embroidery is not uncommon in museum pieces of court wear. Both ladies and mens shoes (especially for court wear) could be quite fancy.

I have worn straight lasted reproduction shoes from [Fugawee's] (http://www.fugawee.com/womens_colonial.htm) and personally they are not comfortable. Others will likely disagree and it has to be said that the longer I wear them, the more comfortable they get. As is the tendency with leather shoes the uppers begin to form to your foot with extended wear. They are, however, not at all uncomfortable, to me. Nothing like an evening in stilettos, which I find to be downright painful! The trick is that in most ways they aren't that different than your modern dress shoe. You just have to imagine how your feet would feel in shoes that are not made to differentiate between left and right. Awkward? Strange? To my modern sensibilities. If I knew nothing else I would imagine they would be quite nice. Better than a bare foot on a cold floor.

The real fun comes in with the fancy shoes. These are mostly for upper class and court wear. You would find the majority of others wearing the simple leather types of shoes, similar (if not in some cases exactly) like the reproductions from Fugawee. These fancy styles were heavily influenced by the French Court. The Victoria and Albert Museum has several examples viewable online from their collections. Victoria and Albert Museum searchable collection. This search shows a few strays that are not from the 18th century, (look for dates in the 1700's) but here are several shoe examples as well as lots of decorative buckle examples.

Here are some of my favorites to give an overview of styles and differences. http://collections.vam.ac.uk/item/O93499/pair-of-shoes-unknown/ http://collections.vam.ac.uk/item/O78894/pair-of-shoes-unknown/ http://collections.vam.ac.uk/item/O135235/shoe-unknown/ http://collections.vam.ac.uk/item/O109236/pair-of-shoes-unknown/

And my personal favorite bit of 18th Century footwear are Pattens. These are covers for the fancy shoes so that they would last longer when outside. They also helped to slightly elevate the wearer and thus the skirt hems just that little bit above the muck and mud. There are examples of these actually being made to match with the shoes. American Duchess is a blog (also a reproduction shoe designer/seller) and here is her entry on Pattens. It does not have a ton of information, but does have several good pictures in one location instead of the various museum websites. For me this is beauty and practicality meeting. You mentioned knowing about the Japanese Geta. Pattens were similar to this in concept and use, though not design and style.

In a related question, I watched Princess Mononoke recently and people are depicted running and jumping while wearing what I assume are geta. How freely could you actually move while wearing shoes like that?

During basic training people suffered stress fractures in their lower bodies due to the strain put on them. This is in state of the art boots with foam insoles and different rubbers to absorb shock.... We have superior technology and nutrition and even then our bodies are strained by long marches.

Be careful not to draw an inaccurate comparison of medical development here. This study itself claims to be the most comprehensive study of stress fractures in the military to date, and claims the earliest documentation of stress fractures dates to 1855.

A corresponding lack of detailed accounts of stress fractures in the military does not mean stress fractures were necessarily even less prevalent in the past, with different footwear. It's possible that stress fractures were as or more prevalent than they are now, were simply not recognized, and left untreated.

It's possible that military training and work itself is a more prevalent factor related to incidents of stress fractures than variations in footwear, for similar reasons that professional athletes also seem more prone to stress fractures than the average population.

The Bata Shoe Museum in Toronto is a great resource for all things footwear, and their semi-permanent exhibit, [All About Shoes: Footwear Through the Ages] (http://www.batashoemuseum.ca/exhibitions/all_about_shoes/index.shtml) is, according the the website,

a voyage through 4500 years of footwear: its evolution, uses over time, methods and materials of manufacture, and its place in our lives and imaginations.

It may be of interest to you.

This may perhaps be more of an anthropological rather than a historical answer, but I think it is worth questioning some of the premises in your question.

"During basic training people suffered stress fractures in their lower bodies due to the strain put on them. This is in state of the art boots with foam insoles and different rubbers to absorb shock."

I highly recommend you check out the book 'Born to Run'.

It's a fascinating (true) chronicle of a journalist who travels to the homeland of the ancient Tarahumara--an indigenous Mexican tribe who are renowned for their endurance.

The author spends a large part of the book marveling at how the Tarahumara runners can not only run back to back ultra-marathons with ease, but do so over rough terrain in thin leather sandals. From the wikipedia entry:

"He asserts that modern cushioned running shoes are a major cause of running injury, pointing to the thin sandals worn by Tarahumara runners, and the explosion of running-related injuries since the introduction of modern running shoes in 1972."

Excellent photo of the Tarahumara running sandal here

As somebody who has done extensive hiking wearing what would be considered pre-modern shoes (moccasins), often carrying significant weight (fifty or more pounds), I find them to be far more comfortable than any hiking boots I've worn, but yes, they suck on flat hard surfaces, like roads. When I go off-road, I wear barefoot runners or moccasins. When I'm in town, I get good footwear.

I'll add that as far as blisters go, I've never gotten a blister walking in moccasins, though my feet have gotten sore.

Not an historian or anything approaching, but I spent most of my childhood barefoot and even if you cannot see it (when you live in town, a cold country or a country where it's not socially acceptable to walk barefoot) your feet have the ability to grow its own sole. At 8 I was able to walk for kilometers in hot sand or concrete without any problem. Even small pieces of glass didn't hurt. I think people from the pre-modern era had far more "solid" feet.