In my Ruby, I had 383/386, with just missing Mew, Celebi, and Deoxys. I lost that cartridge somehow. I've almost had the complete Pokedex in Yellow and Gold once, again just missing Mew and Celebi.
However, I've only beat the 4th Gen games once, and I stupidly decided to let my friend borrow that game. Thus, I could have only transferred stuff from Gen 3 into Gen 4 on that game, and I don't have it anymore.
Overall, I'd say I've had everything at least once, excluding the event legendaries besides Keldeo and Meloetta, and the Black 1 exclusives.
Not changing this sig until The Undertaker vs. Chris Jericho happens on PPV (started October 4, 2009)