say youve been squatting 3 times a week. how about changing one of the workouts to front squat, hell you could change 2 of the workouts to front squat. i hate leg presses, but if you really wanted to, you could squat on monday, front squat on wednesday, and leg press on friday!!! if youve been doing only rows for back, change one or two of the workouts to chinups... substitute stiff legged deadlifts for deadlifts, change mondays workout to 3 sets of 8 for a month, change fridays squat or bench workout to 5 singles, etc, etc, etc.
ive even seen people who after a while on a 3 day a week program, switched to a 4 day split, doing squats and pressing exercises on monday and thursday, back and pulling exercises on wed and saturday. i dont see this as retreating from the principles of the 5 by 5 at all. you are STILL working your whole body, or very nearly so, every training day. squats work the back, they work everything... and deadlifts or stiff legged deadlifts work the legs, not as much as squats, but they still work them. this is in fact the favored program of mike stone, probably the best ex phys guy on the planet and former head of sports science at the olympic training center.
the important thing is to think thru the changes, dont make too many at one time, but make them slowly and steadily.