Usually I just use my FG deck; it's fun to play, though it isn't really fully optimized for the arena. I found that a voodoo deck actually works quite well, since most of the serious vulnerabilities that voodoo decks have aren't really used much in the arena. I was using a 500EM stoneskin deck for awhile, but it's so boring that I gave it up. It was pretty cool to win like 900 electrum a game, though. (and not so cool to lose to 1hp decks because it had no sources of damage!)
I tried the pest deck above (except with unupgraded pendulums) and I wasn't really that impressed. A lot of arena decks use quantum towers, and pest is pretty much useless when each tower provides 3 quanta instead of 1. You have to overcome their upgraded mark as well. I found the deck was just too slow to get going, and didn't deal enough damage or lock the opponent down fast enough. I mean, there's a reason Decay is one of the weakest false gods... too many cards completely shut this deck down, like Sanc or pretty much any shield. (though mind you that's what the steals are for :p)
I've tried supernova weenie decks like the one bluepriest posted, but I find that they're rather hit and miss. Didn't get a supernova or three in your opening hand? Game over. Cremation/destroyers has a similar issue, but I've found that deck to be more reliable, and while it doesn't win a lot, it plays very fast games.
So yeah, I'd recommend either Cremation/destroyer (for speedy games), rainbow control deck (for more wins, particularly EMs, and more fun) or voodoo (for winning more games, but virtually no EMs). Rainbow gets me the most EMs (and therefore most score of the three), and voodoo gets me the most rare spins, but low score/electrum per win, since you'll take a lot of damage before getting the pulled doll out and ready. Cremation is best for taking advantage of those old 1hp decks, and is also the simplest and easiest to play, making it good for n00bs as well as people who are only half paying attention to the game (maybe they are also watching TV or at work or something)