Well i have been very pro MVC the last year, indeed, they have the largest and most up to date collection in Exeter. However, they dropped the ball when they didn't get Nausicaa in! i went next door to virgin (a large collection, but never any new stuff!) and they had 8 copies of Nausicaa and 5 of Cat returns (MVC had just one copy of Cat)
Rather disapointing there. but generally, i'd go for MVC, then Virgin. HMV is improving, but it alone of the three shops still sticks anime in 'world cinema' rather than in its own section, which should say enough on its own.