Fortresses:

-One in your best production area. make it a strike garrison and fill it with armories and barracks. Produce almost all of your troops there.

-Fortresses in far reaching areas which are on a frontline and need defending, but your army is stretched too thin

Enclaves: 

-Cities with lots of essence. Ideally 2+

Towns:

-Next to gold mines and any other financial bonuses

-In sites that have tons of food but not much else

-Anywhere that doesn't fit a fortress or enclave

At the beginning for me it's about tile yields.

The first city that can get 4+ materials will be a fortress.

Cities with 2+ essence will become conclave.

The rest will be Towns.

After the first few cities, adapt to what you have and what you need.

I have to disagree with pretty much everyone who recommends that the fortress is built in the place with the most materials.  The fortress should be the city with the most essence.  The fortress bonuses do not become significant until later in the game.  Until you have researched the techs allowing you to build and improve the forge and the training yard, the fortress troops are not that great - level 2 is trivial to achieve.

By the time you have done your research, and the fortress can crank out great troops, you usually also have aura spells that can improve the attack and initiative of your troops (other stats as well, but these two come first)  This is when you want a fortress with a lot of essence.  Sure, it may be slow at constructing the buildings, and at training the troops.  This is why you have rushing or 'Call to arms'.

So while you may want to build an early game fortress on a material tile, because you feel that you need early trained troops, by mid game you should have a fortress that has 2 or even better 3 essence (for 'Aura of Grace', 'Heart of Fire', 'Aura of Might', in this order) and a lot of grain, so that it can get to level 3 (strike garrison) and produce troops that are truly better.

One good choice for a fortress is a city conquered from the AI.  Because of bonuses AIs get on high difficulties, these often have good essence and great grain.

Completely agree with Tuidjy.

My main Fortress has to have a minimum of two essence, a third is even better.  The enchantments can change the outcomes of battles.  I agree with putting a fortress in a highly contested part of the map, but there has to be a training center.  If you can get the Great Mill and put it in this training center as well.  The minimum Fortress has to be a 3/3/2, but the first number is actually kind of irrelevant to me.  If I can get 4 Materials and 3 Essence, or better, that is my main Fortress.

You only need one fortress, really your best troops will need crystals so you can only build probably one at a time. If you don't use crystal troops you still want a high production place with ESSENCES! There are some super duper bonuses you can put on them with city spells.

My favourite Fortress location is any say 2G, 4M, 3E by a forest. That's what I have in my latest game and I love it.

I also have a town built on a 5 mat forest square that just builds my world wonders, which I rush to unlock. It's my unofficial capital.

Depending on how many grain your Conclaves start on you will need 1 Town per 2 or 3. Most of them should be Conclaves though. Forts do not add very much to your defense, a few crappy cannon fodder troops and mediocre archers, you can also get a catapult. If Forts improved your militia you may want more than 1 or 2.

The best city defense is the Freeze spell. Back it up with Tremor and get your army there quickly.

In my current game, when I got to those spells I was thinking the same thing. Luckily one fortress I captured had 2 essence (3 after I built the scrying pool) and I was able to get the Ironworks world wonder in that city as well. After seeing what I can get out of that fortress is what convinced me that an essence heavy city would be the best fortress location.