I'd give Penn the nod for holding titles in two different weight classes. But his recent losses have somewhat tarnished his legacy.
Frye would probably miss the cut, although I wouldn' write him off as quickly as some others here have. He won two tournaments in the UFC - UFC 8 and Ultimate Ultimate '96, and did so pretty impressively. He also had the fastest KO record hold up for quite awhile.
Miletich definitely, I've called for it several times in the past. He wasn't the most exciting fighter, but he was the first ever WW champ, defended several times, had one of the first great training teams, and did a lot to promote the sport in the early days to get it sanctioned in different states.
Forrest. I guess, for the attention he helped bring to the sport with TUF 1. Does that mean Bonnar gets in too though? Forrest at least wont he title I suppose.
Franklin - No. Why? He held the title and had some good fights, but so did a lot of guys.
Shamrock - I assume you mean Frank, as Ken is already in there. I'd give Frank the nod. First LHW champ, never beaten in the UFC.
Th rest of the guys on your bubble... I don't know. GSP and Anderson will be shoe-ins, and I expect Jones will be too, probably Aldo.