My top three are:
1. Frank Zappa - We're Only in it for the Money
2. The Mountain Goats - Tallahassee
3. Minutemen - Double Nickels on the Dime
Other non-ordered favorites:
Sonic Youth - Daydream Nation (this is rivaling the Minutemen at the moment for that spot)
Neu! - Neu!
Lightning Bolt - Wonderful Rainbow
Whipping Boy - Submarine (I only discovered this one about a couple weeks ago and it's climbed up fast)
Andrew W.K. - Close Calls with Brick Walls
Red House Painters - Rollercoaster
Amesoeurs - Amesoeurs
Atheist - Unquestionable Presence
Repulsion - Horrified
Sleep - Holy Mountain
Melvins - Houdini
De La Soul - Three Feet High and Rising
Xiu Xiu - Knife Play
Neurosis - Through Silver in Blood
Hammers of Misfortune - The August Engine
My Bloody Valentine - Loveless
Gospeed You! Black Emperor - Lift Your Skinny Fists Like Antennas to Heaven
Kyuss - Welcome to Sky Valley
Eric Dolphy - Out To Lunch!
Miles Davis - Bitches Brew
Other favorites that are specifically punk:
Fugazi - Repeater
Flipper - Generic
Amebix - Monolith
Cap'n Jazz - Burritos, Inspiration Point, Fork Balloon Sports, Cards In The Spokes, Automatic Biographies, Kites, Kung Fu, Trophies, Banana Peels We've Slipped On and Egg Shells We've Tippy Toed Over
Dead Kennedys - Plastic Surgery Disasters
Hüsker Dü - Zen Arcade
Wipers - Is This Real?
I could go on for a while listing favorites. Not a lot of my favorites are actually too far down, but that's just how it is. There's a point where bands/albums are well known because they are really that fantastic. That isn't to say that only well known bands can be great, but a lot of those albums left a much larger impression on me then some of my obscure niche dabblings. If I named every album that I loved, then we might be here for a while…