I've been running 5/3/1 for over a year now, and have been making great progress. You really have to read his books to understand what he is trying to help you accomplish. Even after the year I put in, Im still learning, there is just so much information he has in his books. Once you know what your goals are there is a template for you. But he states in his book the philosophy he uses.
1. Basic multi-joint lifts - bench press, squat, deadlift, and military press
2. Start Light - starting light allows you to progress forward
3. Progress slowly - helps you to stay on track, and not sabotage your progress
4. Break PR's - Break Rep Pr's throughout the year.
His percentages for reps and sets are derived from Prelpin's strength chart. And his goals are for athletes not only looking to get stronger, but bigger (hypertrophy), and stay mobile. He understands it takes years to get strong. No shortcuts, no nonsense. you get in get the work done and get out.
Im not sure if I can post a link, but t-nation is where you can find the basic gist of 5/3/1. He also answers questions almost daily on the topic, as he has his own forum on the site.
Hope this info helps some.