A few I've wondered about are these:
Spiritomb > Spiri (like spirit w/out the t)- tomb
Sableye> I've always said Sable-eye but thought it might be Sa-bly or Sa-bley
Lugia > You-gee-uh (where gee is like "Gee, what a nice day")
Entei > En-tie
Treecko > I say Tree-co, but thought maybe it was Tree-echo
Sceptile > Skep-tile. I think someone said they say it w/ a silent 'c'
Lairon > Lair-eon or La-iron (iron like the metal) or liar-on. I don't know
Milotic > I say Mill-oh-tech
Metagross > I say Meta-gros (gros rhymes w/ floss), but I think in the deoxys movie they say Meta-gross (like 'Ew, that trash is gross!')
Roserade > I say Rose-ra-day, but they say Rose-raid on tv and I thought that sounded silly.
Buizel > I think in the Manaphy movie, they say Blay-zul, but I thought it looked like Boo-zul or something. I don't know.
Dialga > I said Dee-all-ga, but then Dial-ga (like 'dial a phone') got inot my head and it drove me crazy.