IDK what Emulation Games is but I can tell you this: unless the game has integrated cheats (like HL2, HTA, Serious Sam series, Saints Row The Third, etc.), you can't use trainers or Cheat Engine. The reason - both the trainers and Cheat Engine are looking for an exe process - for instance: hl2.exe. But in Linux there are no executable files (at least not in the sense you know from Windows) and neither Cheat Engine or the trainer will find the correct process, therefore they won't work.
Whatever happened to the old gamer credo "Winners never cheat and cheaters never win!" ? Ha ha!
In mupen64 - you can use any cheats that are built into many of the games. Either by button mashing, or by entering password style cheat-codes into a text-box. I'm sure there are still some websites that have lists of built-in cheats for a lot of the old N64 games.
If they worked on the console - they should work on the emulated games.
Other than that I don't know offhand. What sort of cheats are you talking about? What format are they in?
Download Game Conqueror for free. Game Conqueror HAS BEEN MOVED TO: http://code.google.com/p/scanmem/ Game Conqueror is a graphical game cheating tool (memory modifier) under Linux, whose main target is to provide functions and user-feelings of CheatEngine. Game Conqueror is written in PyGTK...