Dozens of kinds of fish in Ecco games. Not sure if stuff like the Vortex count, but the canon of the original series points out that they blended into Earth's ecosystem and evolved into things like crabs. The crabs in Ecco are the most brutal I ever saw in videogames ever, so that should count too!
Really shocked no one said Bayonetta. Seriously, that game had awesome fish monsters.
The whole cast was eaten by a giant whale (I know not technically a fish...) in Super Monkey Ball 2/Deluxe, and I remember one or two aquatic bosses in Banana Blitz.
Ghost Squad has unlockable guns based on fish. Deadly!
The Oasis series had a lot of fish enemies and bosses. Each one had water dungeons filled with them.
One of the later versions of Virtua Fighter 5 had a new mask for El Blaze that was a fish. His body on the other hand, is an unstoppable..... WEAPON!
Also in Virtua Fighter 5 (version D) Jeffry has a fish he can equip himself with and if he wins the match he will dance with it.
The second boss of Burning Rangers was a fish.
