Well, for a long time I've been a supporter of guild housing, and everything it brings, so here are just a few of my thoughts on the subject.
Guild housing will be in a half-instanced half-outdoors sort of area. So, you choose if you want to enter your own guild's area or another guild's area from a little tab, like the current PvP flagging but expanded. This is so immersion isn't broken when you see the guild house, and so you don't have to go through an instance for it. I'm sure Blizzard could make space somewhere for this.
Every guild will get a choice on what style they want to build their house, and they can own multiple houses all over Azeroth - completely different styles if they wish. These will be the styles everyone's familiar with, I.E. dwarf, human, troll, tauren, undead.
Guild cities cost a lot more than guild houses, and compose of a main castle in the center - and lots of different buildings around it. I'm not certain where Blizzard could put these. (Maybe on/in a little asteroid in Outlands?) For guild cities, you could have invasions of certain mobs that're native to that zone - demons attacking it maybe?
The guild houses would have "click" points, where you can place whatever you want to place there - like a "click" point for a mounted head.
Now, for the PvP lovers, guilds could flag their cities as PvP on normal servers, whereas they're always flagged as PvP on PvP and RP-PvP servers, and a guild of the opposite faction could sneak in and cause havoc on a huge scale. The other guild would have to have their cities as PvP flagged for this to happen, so the guild could retaliate easily. It will take five hours of not attacking any other guild cities until PvP goes off.
Just a few of my thoughts on the subject of guild housing. I hope you caught the jist of it, because it's rather scrambled.