Here are some suggestions from myself:
1) Make it possible for the guild to pay or collect money from the members. For example, there could be a a soldier/merc guild that needs to pool money to obtain special items etc. Or conversely, there could be a crafting/merchant outfit in which the business owner (IE: Guildmaster) needs to reward his members for collecting material or making sales.
2) Make open warfare between guilds possible. If two guilds are directly opposed to each other, either for territory, resources, faction allegiances, or just fun--they should be able to attack a member of the rival guild at any time. Obviously the leaders of the guilds need to consent to open warfare--but if they both consent--then their guilds can attack each other at any time without warning. So if a player chooses to join a combat-oriented guild, they should be mindful of who their enemies will be.
3) Likewise, make some form of diplomacy system between guilds possible, beyond just warfare. Providing safe-haven to allied guilds, discounts, military alliances, etc.
With such flexible options, you could see players develop their own organizations. We could see trading companies, merc groups, scavenger teams, or independent "Junk-town" like communities forming on their own.