Murder/projectile holes that one person is able to utilize at a time seems appropriate, but things should also be able to be tossed back through them. These "slots" should be marked in some way to represent where they are so there isn't a migration. Maybe (This is going to sound a little silly) there should be raised hoops or something

There shouldn't really be ramparts or raised roof fortifications, because there is no way to properly represent when someone is on top of them. For eample, someone down in the keep shouldn't technically be able to "see" what is going on in a tower or on top of something unless the main building has no roof itself, which would leave it exposed to things tossed over the walls. For example: Billy the Empath is throwing booms from the left tower while Gordon the healer is healing people down in the keep itself. Billy gets hit by an arrow and is knocked unconscious. Gordon shouldn't suddenly be able to get a "sixth sense" that Billy is bleeding to death and be able to run up to the tower to save Billy from bleeding out, but maybe Gordon was going to walk up there anyway to see how Billy was doing?

My other issue with buildings: I notice how most buildings over the last couple years seem to have "translucent" walls and the people inside can see what's going on outside no matter where they are in the building. This shouldn't be possible unless there are big windows which offer further chance for someone to get through them from the outside. If someone is beating on a wall, it's likely people inside can "hear" this happening, but if someone is walking up or standing quietly near the building, it creates a situation where the people inside know he is there, even though they shouldn't be able to see him unless they have someone on sentry outside the building or standing facing a certain direction (since there is nothing on a building that should give someone 360 degree visibility, except for maybe a central tower). By the same token, people outside a stone building really probably shouldn't be able to hear every detail happening inside the building (although one could be cheesy and say the walls are full of holes), but even in that case, the people inside shouldn't know who is eavesdropping. In the case of wood buildings, I don't consider it unreasonable for people to hear what is going on, on the other side, since this is possible on real wooden buildings (like Palmer Lodge, for example). I'm thinking on this because of Mike's description about passwall creating a cheesy roleplaying situation where you know the person is there, but you don't know how you should react realistically in-character. I can't decide on a good suggestion to fix this, other than requiring buildings to have semi-solid walls (like curtains)but that doesn't take care of the other issues.
Doors should either be a great deal more vulnerable than the actual building itself and/or require a reasonable amount of time/people to open and close. A big, heavy door that takes X amount of time to knock down should take a proportionate amount of time/people to open and close. I have seen this abused quite a bit over the last couple years, where someone is able to access the building and quickly open and close a door the same way one would open and close an interior door in a modern house. I think this could be managed somehow for consistancy by requiring a count to open/close a door. Doors should also be properly marked, but I haven't seen a big problem with showing where doors are as I have with magical morphing arrow/magic slits.
Some suggestions may require more work, but I think they should (as part of the responsibility of having something in-game like that) and they would encourage players to come up with more clever phys-reps and add to the ascetics of the game.
I hope none of this sounded snide, I just think they are legitimate problems, especially now that more groups are starting to make buildings. I'm happy to hear any suggestions or current field rules anyone has. Also, with passwall gone, buildings have no "counter."