Considering Guild Wars
I think in order for guilds to wage war effectively and in an entertaining way... it should be something that forces guild members to pay attention to it. For instance if you're in a guild that is waging war, but you don't necessarily want to be caught up in it all you have to do is never engage with those people. However, what if there were intelligence networks. Perhaps in a city you could pay a fee to certain guards that are eligible to send you messages if/when they see members of the guild you're warring with. This would send a notification to all members of your guild that an enemy has been spotted. I think there are a lot of things you could do with this even adding things like counter-intelligence units etc. Perhaps only nodes which the guild has high influence in would they be able to utilize NPCs. Otherwise there could be some sort of jobs board which people get paid or receive items from your guild to report a last seen location for opposing members.
Another thing I'd like to consider is creating some sort of lockout for members. Say that you have recruited intelligence and spent your guilds hard earned money/time on assassinating an opposing member discretely. This could/should lock those opposing members out for a length of time so that it isn't meaningless to do.