Has a pokemon actually "died" in the anime?

Not die and be resurrected, just actually died.

The anime's waahaay too babyish for that. The main characters have never even stepped on a leaf. :P

Well Ash's Charmander almost "died" when the flame on it's tail was about to go out.

As far as I can remember, the Latios from Pokemon Heroes: Guardians of the Water Capital is the only Pokemon to have actually died in the entire history of the Pokemon anime, as he sacrificed himself to save Alto Mare (although, if you start to delve into the Pokemon movies' canonicity, this becomes debatable...) :cer_cry:

I'm pretty sure the Entei from Pokemon the Movie 3: Spell of the Unown dissipated or something to that effect at the end of the movie due to its illusory nature, but I haven't seen that film for a few years...

Pokemon The Movie 4Ever is the only instance I can explicitly recall Sam (Prof. Oak) saying "Celebi, you can't die!", when Celebi was withering away. Celebi got better, of course, so that doesn't really count...

Also, if you consider the "Mirage Pokemon" Mew from the The Mastermind of Mirage Pokemon special an actual living entity/Pokemon, then it could be argued that that Mew perished as well, as it was absorbed into the Mirage System with a particularly devastating attack from a Mirage Mewtwo. Subsequently, its "soul/spirit" held the Mirage Mewtwo back moments later so that Ash's Pikachu could finish Mirage Mewtwo off with Volt Tackle. Furthermore, Professor Oak made a comment about how you can't turn a soul into data, how Mirage Mew was not a 'flawed specimen', and how Mirage Mew was more than just mere data. Although if this Mirage Mew is now in the Digimon-inhabited "Digital World" via the Mirage System absorption, that means that it'll be back again, because the good guys always get reborn at Primary Village! :D

And finally, if you really want to get technical with things, I assume that Charmandertwo, Squirtletwo, and Bulbasaurtwo from Pokemon The First Movie: Mewtwo Strikes Back (specifically, in The Birth of Mewtwo extra feature) also died (offscreen) as well, considering that Ambertwo died and whatever experimental materials and remnants that the scientists salvaged of her were destroyed when Mewtwo furiously destroyed the lab on New Island at the beginning of the movie. (UGH, I STILL NEED TO ACTUALLY FINISH WATCHING THAT "ORIGIN OF MEWTWO" SPECIAL!! :()

In conclusion, Pokemon Heroes's Latios is the only Pokemon that is confirmed to have actually died in the Pokemon anime, to my knowledge. These other aforementioned examples could count as well, which primarily stem from Pokemon movies/specials. Limiting your scope to the Pokemon anime's televised episodes only, no Pokemon have actually died as far as I know, although there have been plenty of close calls (Ash's Charmander from the episode "Charmander the Stray Pokemon" comes to mind).

If you refer canonically (which means those in the anime, and not in the manga or movies), no Pokemon have died. Of course, there are few near-deaths (like Charmender) but none have actually died. However, in the movies, I belive Latios gave up his life to protect Alto Mare from the onslaught of attacks from the revived Aerodactyl and Kabutops.

Also, Lucario have died from my point of view in its movie.