There is no one best way. There are a whole lot of good ways, but the chief benefit of any program comes when you give it up and start a new one. The body responds best to variety.
3 on, 1 off is the way they do it at crossfit.com and it works pretty well. So does 5 on, 2 off; or 3 on, 1 off, 2 on, 1 off. Again, there is no single "best" way.
If you're doing a traditional "bodybuilding" style workout, it works well to group back with biceps, chest with triceps, and legs with abs. Your question makes me think you're looking for a simple program to start with, so try this:
3 days on, 1 off.
Day 1 - deadlifts, pullups, curls. 5 sets of 5 reps of each, with a weight that is very hard to complete the last set with. Preferably 8 hours later, run 5k.
Day 2 - bench,
military press, skullcrushers. 5x5 again. Preferably 8 hours later, do hill sprints for 30 minutes - find a nice hill, sprint up it, walk down, repeat for 30 minutes.
Day 3 - squats, lunges,
decline situps. 5x5 again. If you feel like you need some cardio, try swimming laps for 20 minutes or go for a bike ride. If you have done the workout correctly, you will be happy to
not do cardio for a day.
Eat meat, eggs, fresh fruit and veggies, nuts...period. To drink, you get water, and lots of it. The diet is by far the hardest part of this whole thing to accomplish, but a clean diet will pay off with huge dividends - far far FAR more than lifting hard without a clean diet.