I can't really pick my top three bands, but here are the ones I'm really into right now:
Led Zeppelin
Black Dog
The Battle of Evermore
Dazed and Confused
No Quarter
Kashmir
The Rain Song
Misty Mountain Hop
When the Levee Breaks
Moby Dick
The Lemon Song
Alice In Chains
This is just about impossible, so I'm going to cheat and go hard rockers first, then soft stuff
Hard stuff:
Down In a Hole
Love, Hate, Love
Grind
Man in the Box
We Die Young
Dirt
Them Bones
Rooster
No Excuses
Rain When I Die
Softer stuff:
Don't Follow
Heaven Beside You
Brother
Got Me Wrong
Am I Inside
Right Turn
Over Now
Rotten Apple
Nutshell
I Stay Away
Tool
Again, hard to narrow down, but here goes:
Stinkfist
Eulogy
Opiate
Parabol/a
The Grudge
Ticks & Leeches
Aenema
Hooker With a Penis
Pushit (live)
Prison Sex