The new bookmarks seem good to me! Now I have to go through and sort mine...
A notes option would be kind of nice, but I see how that could be tricky to implement, plus I'm sure there would only be a few people who would use it these days.
Glad you were able to find some maps to work with. I see why Blender would be tougher to use since you want to preserve lightmaps. I definitely agree with your taste in Quake 3's style - even though it's old, I still think some maps can look heaps better than more modern engines. Some maps have an atmosphere that just can't be beat by any other game in my opinion.
GTKRadiant isn't really modelling software, it's a level design tool similar to something like QuArK or Hammer. However in your case, you would sort of be using it as a modelling tool. Why not just use Blender instead? It would probably be more straightforward and less of a hassle to export.
If you are meaning to take some maps from here and port their geometry into a whole other game, I'd say it's a bit of a grey area. You'd definitely want to contact the map authors first (though I wouldn't be surprised if half of the emails you find are closed by now). You can find an author's email in the readme file in downloaded zips. Many readme files have the obligatory "do not distribute or modify in anyway" disclaimer, so you'd probably be out of luck in those cases. You would also have to be careful with textures/models/sounds/other assets - if some maps use vanilla id textures or textures from other authors, things get more complicated.
Personally I wouldn't recommend grabbing maps from here and sticking them in your own game, you should probably just create your own levels from scratch.
Fog can be finicky sometimes. For orange fog, try the fog_timdm2 shader in sfx. There are some others similar to it (the ones with white "FOG" text on a yellow background), so see which one works best for you.
On a different subject, I also wouldn't mind a "map favoriting" system. What Tig described seems great to me:
Very good point. Though I think the majority of his "reputation" was gained before he posted the stolen map. I'm also pretty sure his bio is 100% lies, as I can't find anything related to those claims.