I agree completely with Trumpcard -- diff is the way to go. Also, you'll want to use the command line options -Naur to create "proper" patch files (which can be used by the unix tool patch). So what you want to do is run in the directory above the EMU directory
Code:
diff -Naur eqemu-original/file.txt eqemu-working/file.txt > patchfile.txt
(assuming that your changes are in the eqemu-working directory and the original is in the eqemu-original directory)
Then, to apply the changes in patchfile.txt, you go to the EMU directory and run
Code:
patch -p1 < patchfile.txt
You can also have changes to multiple files or whole directories with the same system (just give the directory name instead of the file name when running diff).
You can get both diff and patch with cygwin if you're running Windows. The GNU utilities are really nice, even if they take a little time to get used to.