Sorry if I posted too late, but here's a few I'd like to share.
Arcanacra - Fun throwback to vertical shooters, created by one of my favorite japanese freeware developers, KEIM.
http://www.yomogi.sakura.ne.jp/~si/S...ra/v04_e.shtml
Cube Colossus - Different twist, almost arena styled. It also has an actual plot!
http://www.kongregate.com/games/lucidrine/cube-colossus