Great thread idea. I'm not an expert or anything, but I'll share my opinions and ideas.
For starters, a building has got to have a base of some kind. The pre-made buildings that came with the starter set had no bases, which made them pretty fragile. Bases are a MUST.
Floors. I find that 2" to 2.5" is a good height from floor-to-ceiling for each level. When it come to how many floors, the sky's the limit, really, but when you keep in mind how long it takes in-game for a model to climb a really high building, you may just realize that a 3' tall mega-tower probably won't see much action towards the top. I usually limit myself to 4 floors.
Doorways that I've made are 1.25" wide and 1.75" tall. This seems to scale well with standard human miniatures. With windows at ground level, you have to consider whether or not you want models to be allowed to climb through them or fight on either side of them. Also, from a flavor perspective, ground level windows are most likely to be boarded up, because looters aren't as likely to climb into your shop from the 5th floor windows.
Ladder and stairs are important, especially if you want to encourage players to climb around on the upper levels. But still, it's overkill to have so many ladders (like 3 in each building) because then it makes climbing rules irrelevant. This is supposed to be the ruined city of Mordheim, and it's not like there's someone that came through and demanded that it be up to code with wheelchair ramps and everything. Instead, try and make above-ground connections from buildings with stairs to those without.
And finally, the city of Mordheim is supposed to be cramped and dirty, full of narrow winding streets, etc. At the same time, you have to be able to actually fit your hand in there to move models around, especially during combat where models are getting knocked down and stunned on a frequent basis. The less open and accessible the building is, the more likely it's going to be clumsily knocked around as one your fellow gamers struggles to move his models around inside. If your street is less than 3" wide, get ready for a building to be knocked over.
Remember the 3-story red building from the boxed set? The one where you need chopsticks and a dental mirror to move around insde? That's a good example of a building not being open enough.