I only like the bosses of the temples.
So, I like:
Morpheel
Argorok
Stallord
Molgera
Twinrova
Odolwa (because with the FD mask you kill it in three hits )
That two/three headed dragon in PH, ALTTP and a few other games
Puppet Ganon (because that last form was so freaking annoying)
...I'll edit this post as I think of more.