For me the best DoaM game is Nexus Ops. Yeah it's cliched to sing it's praises, whatever...the game is a stroke of genius. It made DoaM games HIGHLY aggressive and made it so they didn't have to be an 8 hour slugfest. Its impact can be seen in pretty much every DoaM game to come out in the past 5 years that's worth playing.
Chaos in the Old World - If this counts then it's probably my number 2. One of the best games ever made.
War on Terror - I was glad to see Barnes mention this long lost relic. Yeah, it's hopelessly dated now, but holy shit was this game fun. And MEAN. I still have fond memories of this one and would gladly play it. Dropping dirty bombs on people while wearing that "EVIL" balaclava will never get old.
Runewars - This is another great, great game. It does so much right. I really need to get my hands on the expansion.
Senji - This is a weird one. It's set in Feudal Japan, designed by Bruno Cathala and most people have never heard of it. The game requires a full compliment of players to really work, but it has a lot of interesting ideas. It's not straight conflict as you can win through other peaceful means...but the game lets you be a devious asshole so I like it. Each round there are secret diplomacy-esque negations among the players where they trade cards and discuss alliances. You can trade goods, give armies in support...you can even give family members away as sign of trust. Then later on, the person can just flat out kill your grandpa. The game is all sorts of strange ideas....it's certainly not best in class, but man it wins points for being this oddball amalgamation of a Euro/DoaM, "nobody loves me" bastard child.
War of the Ring - Don't need to say much here...This game rocks.
Starcraft has many moving parts, but two great/different things: the reverse order system and the deckbuilding style card combat. Forbidden stars looks like it keeps the first and loses the 2nd.