I've been going to Phoenix Comics for about 15 years now and they've remained a favourite.
It was great going here as a kid, the staff were fun and would give us loads of goodies. They even introduced me to Lupin the 3rd, which is a huge favourite of mine :)
And it's still great going now.
Their selection of anime and manga is second to none in the city. They also have a great selection of toys, figures/statues and comics. Oh and don't forget the record store that is part of it! They have tons of randoms for $1 and all sorts of re-presses, rare records and CDs.
Prices are pretty standard for the city, but I've nabbed some things for absolute steals before (I got a clearance figure for $55, which sells on Mandarake for over 20,000 yen) Their prices on anime beat most of the other retailers as well, come here instead of being utterly gouged at HMV.
The only knocks I can give it are the fact that it doesn't really have back issues and it's dangerous here for me. I can spend so much money here so darn fast! Oh and it's worth mentioning that the staff can be really icy at times, but they will help you if you ask so don't be shy.