Gen 1: Starmie >> Suicune = Skarm = Jirachi
Gen 2: Skarm > Suicune > Starmie >> Jirachi
Gen 3: Suicune > Skarm >= (?) Jirachi > Starmie
Gen 4: Starmie > Jirachi = Suicune > Skarm ???
Given that, I'd say Starmie should get #5, I'd say it deserves more credit for existing in RBY than Skarm/Suicune for being top in gens 2/3 (Starmie is still middle-OU in both afterall).
Followed by... Suicune? That one's hard though. At least I think both skarm and cune should clearly go before jirachi.
And what about Raikou? How good is it in gen 4? It should go before Jirachi imo.
And the already mentioned Chansey/Blissey/Chanseyblissey. Or is it #5 already?
EDIT: I'm happy with Skarm at 6.