I like not using the masterball. It makes me feel like I actually earned it. It makes the fight more memorable and satisfying.

Guide to legendary battle if you don't want to use the masterball.
1. Save in front of the legendary before initiating battle (Note that this doesn't apply to roaming legendaries).
2. Throw a quickball. (for gens 4 and up) (if not caught please precede to step 3).
3. Whittle down the legendaries health to red without killing it.
4. Inflict a status condition that won't slowly kill it Either paralysis or sleep. (note steps 3 and 4 can be swapped).
5. Chuck ultra balls like a madman! (dark balls can work if in cave)