From my experience of Warhammer to GW2 it has wound up different in each game due to the game itself. We LOVE when we can get everything into as little separation as possible. Fog knows way more than I do on how guild and alliances are being planned along with the communications channels to go with them.
Here is what we did in the games I have played:
Warhammer - Gasicioch was actually in three guilds with 500 character max, but 10 guilds could be in an alliance. There was great guild and alliance and private channel networking in that game. We had what we called the Tuatha, which was the extended family, and a chat channel for this. This allowed some 30+ guilds to be affiliated with Gaiscioch. I actually ran or co-ran two different guilds in Warhammer that were Tuatha members and it worked out well.
Rift - unlimited guild size - not a problem with things in game for the guild and decent enough chat channels to run our community events.
GW2 - by account, but 500 max. We would have been in trouble if it was by character like Warhammer because of us altaholics. Unfortunately we never got an alliance setup in the game or a way to do personalized chat channels. There has been a lot of tweaking of the guilds/ houses trying to find the best way to keep things organized and as homey as we like things to feel.
Fog, correct me if I'm wrong on any of these, but this is pretty much what I remember on in game guild, alliance and chat setup.
Of course, we always have a voice chat setup, as well, to help with organizing things.
Here's to a decent guild, alliance and chat setup like I remember in Warhammer with the awesomeness of a three way PvP like GW2 and DAoC and some really cool story PvE when we get to ESO. They're still rocking our crazily huge family needs better than other games Fog has got us into watching and testing.