DC Universe does a lot of things really well, but building easily-navigable hangout spots is not one of them. The Justice League Watchtower and Hall of Doom serve as the primary meeting points for all Hero and Villain characters, respectively. Both house a ton of useful objects—like the Phase Shifter, which allows you to swap between PvE and PvP phases of the server at will—but not all of them are easy to find.
The cryptically-named RedDragon74 over at DCUO Life has done heroes a great service by putting together an all-encompassing map that labels the locations of everything you'll need in the Watchtower and also provides a full list of bounty locations and a complete breakdown of how to earn the different PvE currencies at endgame. It's not the prettiest map ever made, but all the info is here.
Unfortunately, there doesn't seem to be an equivalent for the Hall of Doom quite yet (sorry, Villains), but the endgame breakdown list should still be able to help ne'er-do-gooders.