Well I don't give a flying R9 if a game is a conversion or not, I'm voting for the game which I like the best out of the nice big list that FreakyWeakyWoo has taken the care to type up.
R-Type for me because I bloody love it, it doesn't matter that's it's a conversion because it's a damn fine game. And besides, there really was no other way for me to play R-Type in such good form. Although the MS one is a damn fine conversion.
And I gotta agree with Akira, Battle Squadron is a much finer game than Blood Money, even though I'm not a huge fan of BS. It's just Blood Money feels so amateurish. The ships, the bullets, the sound effects all just seem a bit... weak.
GO R-TYPE! The best horizontal shooter ever created.