Okay, so we all know that Sega is the master of Fish-related fatalities and general aquatic violence, so lets put together a master list of all dangerous fish in Sega games:
Bayonetta"
"Really shocked no one said Bayonetta. Seriously, that game had awesome fish monsters." -Sanus
Burning Rangers"The second boss of Burning Rangers was a fish."-Sanus
Dynamite CopYou can kill enemies with Sushi (which is Raw Fish).
Ecco the DolphinIn Ecco the Dolphin 1 and 2 you play a large Fish that can kill enemies with air-blasts from his snout.
"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!" -Sanus
Eternal ChampionsIn this one level, you can knock the other dude into the water and he gets killed by Fish.
Ghost Squad"Ghost Squad has unlockable guns based on fish. Deadly!" -Sanus
The House of the Dead "In House of the Dead 1 there are those things coming out of the fountain right at the beginning." -crackdude
The second boss of The House of the Dead 2, Heirophant, is part-Fish.
Last BronxZaimoku beats people into unconciousness with a large Fish.
Red-Eye knocks people out with Sushi sets on a stick (Raw Fish)
NiGHTS into Dreams"In NiGHTS into dreams... there is an ugly fish called Gulpo trying to wake you up." -orta
Phantasy StarDe Rol Le (and his girlfriend De La Rie) in Phantasy Star Online. They look like eels or something, but they are underwater, so they count? -Orta
REZ"There were these crazy robo-fish in Rez too" -SOUP
Ristar"Fish enemies in the underwater segments of RISTAR" -cubeb3
Sea ManLeonard Nimoy is a talking Fish, who could probably kill you.
Sega Bass Fishing/Sega Marine Fishing"Fish who break the line!" -crackdude
Shining Force III: Scenario IIIThere are Flying Fish that can kill you even out of the water.
Skies of ArcadiaThe massive weaponised space-ship in this game is named after a type of Fish (Delphinus).
"I know that whales are technically mammals, but this one played a pretty big role, and did some killin'.
Rhaknam from Skies of Arcadia" -SOUP
Sonic the HedgehogIn Sonic 1 & 2 there are robotic Fish that can kill sonic.
In Sonic 3 there are more robotic fish, but these ones can become invincible with spikes, or latch onto Sonic as well.
"Also, the Orcas in Sonic Adventure 1 and Sonic06.
In Sonic Heroes, Robotnik's airship is a whale." - crackdude
"Sonic Adventure 2 Green Hill Zone,
Kill the RoboFish from the orignal STH. Also I am sure Knuckles can kill aquatic creatures in some stage I think it was Aquatic Mines." -cubeb3
Story of Thor/Oasis"The Oasis series had a lot of fish enemies and bosses. Each one had water dungeons filled with them." -Sanus
Super Monkey Ball"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." -Sanus
Virtua FighterDural fights you underwater in Virtua Fighter 2, so she is likely part-Fish.
"Don't forget the "satan shark" from virtua fighter. Jeffry'll catch it one of these days." - kozmo
"In VF Kids there is a translucent version of Dural where she has a fish inside her head." -Orta
"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." -Sanus
Virtua Tennis"In Virtua Tennis for the GBA, there is a mini-game called "Burger Chef" in which you hit balls at a grid of burger items. Hit the grid, and you earn points. Miss the grid and you get giant fish heads stacked onto the bun. The heads are "lethal" in that they give no points, take up a spot of a real ingredient and "kill" your game resulting in an eventual failure." -Barry The Nomad
YakuzaIn Yakuza 1, Nishiki has a Fish tattoo on his back, which granted him Fish Powers.
In Yakuza 3, You can use a giant Tuna Fish to knock out opponents.
Please contribute with more lethal fish from Sega games, so that we can create the most comprehensive list on the internet.