There are soooo many good schools here. I'd definitely recommend checking them all out and seeing what you like and what fits your needs/budget/schedule.
Gracie Barra Vancouver - I'm biased to GB as I work there, but I really like it. Great BJJ coaches (Black Belts from Brazil, a Brown Belt and a high ranking competition Purple). Boxing coach from Mexico and we have Muay Thai a few days a week too. We've done pretty well in MMA (undefeated at Battlefield and NAC) though that's easy to say with only 3 fights so far. Our Stand Up team does pretty well at Muay Thai/Kickboxing tournaments too.
Dynamic MMA - out in Richmond, great guys from the few times I've dealt with them.
Iron City Muay Thai - Jason Fenton runs it. He's a former World Champion in Muay Thai and he's a really cool, funny dude. I hear their BJJ and Wrestling are good too.
Clinch MMA (Burnaby). Not a "big" gym, but Snickerz is a solid coach and they have success in MMA comps. I used to train there and I quite liked it.
West Coast BJJ/MMA - I trained here too (when they were affiliated with Clinch) and really liked them. A bit different as far as class structure goes and some of the coaches are younger and maybe a bit "brash" but pretty solid team overall.
Also, Franco Pankration. Don't know a lot about them but whenever their students come train with us they always impress me.