The Bill Starr/Pendlay/Rippetoe 5x5
Madcow's Geocities Site - A great resource for anyone interested in training for functional strength. Read as much of this as you can digest.
Madcow's Site
Westside Barbell (WSB)
Westside is entirely a powerlifter's approach to lifting weights. It's concerned with one thing and that's increasing your 1RM on Squat, Bench and Deadlift. It uses the conjugate method of training and there is no Westside program, as such. That said it's as flexible as your ability to identify your weaknesses and can be customized for the common man.
Korte 3x3
Deepsquatter Archives
The Korte 3x3 is in the upper-right corner and is a brutal periodized program concentrating solely on the big three lifts
HST - Hypertrophy-Specific Training
Hypertrophy-Specific Training : : Official Home of HST
DFHT - Dual-Factor Hypertrophy Training
AnimalMass's DFHT program?
I've seen it recommended that you should stay away from this until you can squat at least 1.5x bodyweight. Another fairly brutal program.
DoggCrapp Training
A fairly advanced program concentrating on heavy weight, training to failure, progression, rest pause and extreme stretching.