I'd say CE, but the only reason for that is the overwhelming experience you got from first encounter. That feeling was never as strong in the following titles, although gravemind was sick af story-wise.
I voted for CE flood before I read the bottom text... which means my true answer is Halo 3. There's more variety with the pure forms and the way they fall apart when you melee or shoot them in certain parts of the body is a cool mechanic that was done so well in that game. It felt more in line with the fact that the Flood is made up of flimsy, decomposing bodies.
Well, it depends on what exactly we're judging. I can't stand to play against Halo: CE flood. I prefer later games when you can more easily disassemble and cope with them. Later games made them feel like the nasty puss sacs they are, as opposed to immortal rocks. Presentation wise, however, hmm... I guess I'd stick with Halo 3.
Gotta go with Halo 2... the sound effects, the atmosphere, and overall terrifying appearance of the Flood in that game give it the edge for me. Another huge factor is that we see the Gravemind for the first and only time in the first 3 games.