I suppose you could put cranking noises into 5 categories: Click, scrape, and Snap, pop, and grind.
Anyway, start with the pedals. One thing to try is lubing the springs/mechanism that holds your cleat in the pedal. That usually is a click. Lube the springs and sort of work it in by flexing the pedals.
Next, make sure that the pedals are tight to the crank.
A Snap is usually caused by the skewers. You can wrench on the bike so hard that you can be moving the rear wheel slightly in the stays. Make sure those skewers are nice and tight.
Now, if it doesn't make that noise when you're cranking hard and standing, but does when you're sitting. Tighten up the seat and seat post collar.
A pop & grind can be caused by the Bottom bracket. I'd replace the BB as a last resort, but generally a lot of shops take it off the bike, clean the threads, lube it up real good and put it back it. If you turn the cranks with your hands and feel some grinding or hitching in the motion, it may be a bad BB.
Anyway, go with the easy stuff first. Pedals, Skewers, and Seat/Seat Post.