n64hijack is a command-line executable that allows you to easily insert some assembly to be run right before a N64 game begins.
Usage is n64hijack infile outfile asmfile [--noWatchKill] where asmfile is the assembly to run at the start of the game. Adding the --noWatchKill argument disables the functionality where codes that write to WatchLo and WatchHi are automatically NOP'ed. In commercial games, writes to WatchLo and WatchHi are undoubtedly attempts to kill GameShark-type cheating devices. Leaving WatchKill enabled removes the need for F1-type codes, but may cause issues if a homebrew game relies on them.
patcher.asm is an extra file included with the distribution of n64hijack. It demonstrates how to run code every time the general exception handler is called in an N64 game. It implements a GameShark-like cheat engine using a technique based on the work of parasyte in his alt64 project. It should be easily modifiable to allow you to insert your own code to run at the GEH and cut out the GameShark. Alternatively, you can keep the cheat engine and bake GameShark cheats directly into a ROM - there's a section at the end of patcher.asm to add in these cheats.
IMPORTANT - some of the methods used in patcher.asm assume that the ROM being patched is a commercially-released game and not a piece of homebrew software. Additionally, hijacking the GEH as implemented in patcher.asm this will not work on any emulator except for cen64. Hijacking relies on WATCH exceptions, which no emulators outside of cen64 support (as WATCH exceptions are usually only used for debugging).
n64hijack relies on the u64asm assembler by hcs. It's not a perfect assembler as it still contains some bugs with pseudoinstructions (notably li and a lack of an unconditional branch, b), but it's the best assembler available that doesn't require the installation of a large toolchain.