BKGaming: Nobody can really say for sure, most likely though this will depend on the devs of the said game. GOG seems to have more control over the games than say Steam does.... but this isn't something they would likely do.
Yeah, I don't think that there's been a single case where GOG actually messed with a game's source code or have done any notable alterations to games, I think so far GOG's own work has been limited to making games work (and I think that's a good thing).
There were some signs that GOG is going to pursue reverse engineering actively themselves soon (IIRC someone spotted a job listing that hinted at this fact) but what they are going to do with these skills and resources is anybody's guess at this point. I for one think that it's still just about making games work, not creating HD editions of their own.
hucklebarry: Figured as much, but I guess I'm thinking in terms of games with heavy mod-ability, such as Thief. Since fans do have the tools (including the raw original missions) could the Galaxy launcher allow this?
Modding tools can only do so much. I'm no expert but I doubt that any "highly moddable" game is actually moddable enough to add this kind of functionality. I don't think you can implement such an API without altering the source code but others may correct me if I'm wrong.
hucklebarry: Thinking way outside of the box, could we see a system that lets you download custom achievement files for various games like Thief, Unreal Tournament, Deus Ex, etc. (games that are heavily moddable).
Even if GOG got an okay from the games' rights holders to do these kinds of alterations, as I said: GOG is so far all about making games work, not improving or extending games themselves and I doubt that's gonna change. Really expect achievements to be added the same way it happens on Steam: via HD editions developed by either the original developers or whoever got hired by the publisher for this job.