Essentials - Many, many server commands, and a rudimentary economy.
PermissionsEx - Much nicer permissions management than that built in to either Bukkit or Essentials.
OtherDrops - So many plugins based around changed the drops of one item or a handful of items, this does it all in full granularity. My zombies drop cookies, and jungle tree leaves rarely drop cocoa beans. I also have coal, lapis, and diamond ores drop only one item with an iron pickaxe, to encourage the move to diamond tools. (My economy is fed solely from "bounties" on mobs: mobs have a chance to give you economy money when you kill them.)
Vault - You won't do anything with this: just have it so other plugins can link into your permissions and economy systems. It's a compatibility layer only.
LWC - Provides the most-familiar chest and door protection to users of SMP servers.
WorldEdit - It will save you THIS MANY TIME.
WorldGuard - It will save you THIS MANY GRIEF REPORTS.
Command iConomy - Use this to turn "cheat" commands from Essentials into pay-for services. Want to let people change the weather? Charge them in-game money for the privilege!