I have 3D Space Harrier, Super Hang-On, Altered Beast and now Galaxy Force II.
3D Space Harrier, as an auto-stereoscopic version of the 1985 coin-op arcde game is awesome, but as a game in general, I like Galaxy Force II a lot more than Space Harrier. The same for Super Hang-On as well as After Burner II, ( 3D AB II is coming to the Japanese eShop on Dec 18th) You really ought to buy 3D Super Hang-On because it's so awesome.
I was pretty disappointed with 3D Altered Beast but because, first of all, it is based on the MegaDrive / Genesis console version, not the System 16 arcade, and it does not have a very good auto stereoscopic 3D effect outside of the console version's parallax scrolling layered backgrounds, which according to the interview were added to for 3DS but so far I don't see any extra layers. So I'm not sure if I should buy 3D Sonic The Hedgehog right now because I question whether or not its 3D effect makes it worthwhile, since it too runs on M2's MegaDrive emulator. That said, I'll have to buy Sonic eventually anyway to show my support for SEGA and M2 (I want 3D After Burner II and whatever others games are part of the second series) but I dunno if I'll end up spending a lot of time with it.
3D Space Harrier, Super Hang-On and Galaxy Force II are all worth $5.99 / 4.99 / £4.49 a piece.