Frankly I don't know a whole lot about the disk system. I do know the disk belt is likely to break, so that's something to look out for (it is repairable though).
For specific games there are a handful of cool ones, but some are already available in cartridge form for the NES so it's kinda useless to go for them (like Metroid, Kid Icarus, both Zeldas or Castlevania). The ones I know about that are good are Super Mario Bros 2 (AKA lost levels), Nazo no Murasame Jo, Biomiracle Bokutte Upa (exists in cartridge form but it's more expensive). You can probably find some more if you look around the interwebz
Congrats on your find!