There are a bunch of special encounters not listed here, and since I'm trying to catch them, I thought I'd post the ones as I come across them. Do note that I am no where near close to completing the game as I only have 7 badges at the current time. So I don't know if these have deadlines or not.
murkrow: aqua gang hideout, windy, night (can know brave bird or perish song as it's egg move, be warned)
houndour : magma gang hideout after winning as aqua gang and who know how many badges (it wasn't there when I looked around the gang with 4 or 5 badges.