There is a computer in the "Lazarus Labs" level that when interacted with will play a Doom style version of Bejeweled. It can be found in the room with the DOOM Guys crypt on the left side .
The Dopefish can be found as the logo on boxes of ramen noodles from "Dopechan Noodles" found in various areas.
Progress in the single player campaign until you reach the final Boss. Quit and replay the missions to get the collectables.
At the start the game in the Prologue where you wake up and leave the area he was kept in, look at the bottom of the security door. You can see that a Mixom Manufacturing sticker has partially slid down, revealing that it was covering a Vault-Tec logo.
During the "Titan's Realm" mission, you will encounter an area where you can see a large number of enemies and a yellow booster platform at the back. Walk the stairs to your right and follow the wall along the second floor to the end. There is a hidden room is behind a crack in the wall that you can jump up to reach. Although it looks like it is too small to get through, you can enter the wall .