Given my current infatuation with org-mode, I would accomplish the function you describe
above (only) using org-mode. I would make each command a radio link, such that you could
hypertext jump to the documentation on the command wherever it occurs in your program. I
would take a file of command documentation and insert it at the end of my program. Each
command name should be enclosed in<< >>. The turn on org-mode.
Alternately, I would suggest writing a lisp function which parses out each
command and replaces it with a link with the same text as the label and that
link executes lisp code to bring up the definition, in the message area, a help
buffer, new frame or whatever fits best for you.
Have you checked out asm-mode? That might give you syntax coloring for assembly
that could be useful. You might have to create an child mode with custom syntax
table, depending on your assembly language.