I noticed that the CD32 and Amiga sets you have listed are quite out of date. The latest CD32 set was released in December 2008, and the latest version of the Amiga ADF sets is from around the same time. Have a look on Pleasuredome to see the most up to date sets. And also visit toseciso.org to get a copy of the latest TOSEC CD ISO dats (current dat download also includes all the current cue files too, which is very useful when updating existing sets).

And to speed up the download of new sets, from places like Pleasuredome and Underground-gamer, it is worth using the dats on your existing collection with CLRMAMEPro and using the program to rename your existing sets to fit the current release. That way when you then join a torrent and point it at your existing set it won't need to download as much to bring it up to date.

As for which is the best type of set to download, it all depends on the platform. For the Amiga the TOSEC sets are far more complete than any of the others. But for others like Amstrad or C64 the Good sets seem much more complete. It is best to check the dat files for the sets available for each platform and see what the differences are to make the best choice.

Then you also have specific sets, such as the Gamebase sets, which are specific to their own frontend and therefore only include the supported files and games in the set, which means they will be missing quite a lot of unsupported stuff.