I'm not one to usually say DCUO did something right but with the announcement of Garrisons in WoW you have to admit that the player bases introduced a few years ago into DCUO can be considered a precursor to them. To explain for those that don't know, Player Bases in DCUO are instances that only YOU and someone you invite can enter and they house a variety of both scenic items and items with use. These include vendors, crafting stations, a respec machine, sparring targets to test builds, and a machine that gives out boosts based on the base supplies you have.
WoW has expanded this even further with the Garrison. On top of its version of these, you also have buildings that mine/gather crafting components and the holy grails of the system: A small legion to summon every few minutes for a NICE burst skill (number of soldiers summons increases as you level the garrison) and a Sortie minigame that basically sends out "champions" of your garrison to go do missions to get new upgrades or some other stuff..
Now Player Bases/Homes have been a very highly requested feature, if only because its a staple of the Superhero Genre. I'd like to, when implemented, have them serve as more than just personal instances and would love for you to draw from these examples, if only because it would be a nice In-Sink.
Plots/Patrols - Just as Batman has the Batcomputer, you'd have a super machine (or orb of scrying or whatever..) which basically allows you to start small arcs leading into a large finish. Villainous characters will begin plotting to kidnap world leaders, super weapons, conquest, etc and start off in missions to gather necessary components or case the area. Heroes would be alerted of a mission that leads into uncovering similar plans to the villain missions.
The Armory/Suit-up - What's Tony Stark without his gallery of suits? Here you would see your saved costumes for that specific character and gain access to the tailor to change anything or make a new one.
Followers/Henchies/Allies - What is a villain without his Loyal Followers? Or a hero without those ungodly amount of Longbow to back them up? (GRAAAAAAAAAAAAAAAH! *rage*) Here you would customize and create your own small personal force of no-names and expendables to call out for in the open world. Want to bring them into your missions as friendly NPCs? Go ahead! Just be warned that the mission will scale dramatically to that. Don't want to? Just check the box saying so.
R&D Area - Here you can create temp powers, boosts, enhancements, costume pieces, ETC using items found in the open world.
Memorabilia - "Hey, that's a cool giant penny you got there, Batman. How'd you get it?" Completing badges and mission arcs will unlock more things to pile into this gallery. Really enjoyed a certain arc? How about you interact with the memorabilia from that arc and be given the opportunity to do it again!
Roleplayer; Esteemed Villain