Dolphin Blue
Knights Of Valour
Hokuto No Ken / Fist Of The Northstar (awesome!)
Metal Slug 6
Neogeo Battle Coliseum
Rumble Fish
Rumble Fish 2
Samurai Spirits Tenkaichi Kenkakuden
The King Of Fighters Neowave
The King Of Fighters XI
These are the ones I'd get. I've never played Dolphin Blue, but heard good things. It's a Metal Slug rip-off. Ditto on Knights Of Valour, but it's IGS, and they usually do well enough.
Keep in mind that there are PS2 ports for KOF Neowave, XI, Tenka, Hokuto No Ken, Metal Slug 6, The Rumblefish, and NeoGeo Battle Coliseum, so I wouldn't pay too much for any of those. None of them struck me as being better in arcades; the Atomiswave is basically a Dreamcast, so there's no real technical problems. Actually, Neowave, Rumblefish, Tenka, and XI are better on PS2, since they have faster load times and/or more characters.
I'd definitely get The Rumble Fish 2. It never got a home release (the original on PS2 has two characters from the sequel, guess they felt that was enough) and is an awesome fighting game.