I actually really enjoy this question, because it's one of those things that you can let your mind soar with if you're a roleplayer. My main (and my guild) are very anti-Scourge and pro-reclaiming (and colonizing) Northrend, so Wrath is a fun time, and perfect for envisioning my guild in that sort of position. My character would probably do something dungeon-related, maybe in Icecrown, where the Scourge population is thickest. I could definitely see an escort-style quest, where my usual 5-man group in NPC form fought alongside a 5-man group of players in a Zul'farrak style encounter, fighting off waves of undead. After that encounter, those NPCs would 'hold off' more Scourge while the main party forges ahead to take out the boss and save the day.
My guild overall would be a faction tucked away in Icecrown somewhere, working a wedge into the Scourge forces so the Horde and Alliance can get a foothold. The daily quests would involve three things: Siege weapons, explosions, and lots of fire.
My friend and I would both love to see an old guildmate of ours that passed away get his moment in the spotlight, implemented as an NPC in the Dragonblight that hands out parachutes at the top of Wyrmrest Keep. He was a big fan of Dragon lore, and had a tendency to fall off of things in-game. It would mean a lot to us, and be really fun, too.
How about you guys? What would you do? Does your guild have a story that you would love to see implemented for all to see? Heck, even you guys with PvP-centric guilds can get in on this. Can you say 'mercenaries'?