How did I miss this thread until now?
Anyways, okay, my top 5... and I'm going to cheat by listing making two-parters as 1...
1. Gamma Ray--Land of the Free
2. Avantasia--The Metal Opera
3. Helloween--Keeper of the Seven Keys
4. Sonata Arctica--Reckoning Night
5. DragonForce--Valley of the Damned
Man that was hard and I missed so, so many amazing bands. Other people have covered 'em, though. But that's my top 5. (Man, somehow I didn't get Guardian or Falconer in there...)
Also, re: before, The Fourth Legacy is the first good Kamelot album. I can't listen to their stuff from before without quickly boring of it. But most everything after Khan started writing songs is solid gold.