Every coach that I know wants his offense to be run in transition. Running 2-on-1, 3-on-2, 3-on-2/2-on-1, 3-on-2-continuous drills are common place. I ran them as well. However, they never served the function that I wanted them to. 3-on-3-on-3, along with its progressions, is a great tool for sharpening your transition game, half court offense and even your defense.
2 on 1 Fast Break Drill is an extremely efficient way to practice the skills and decision making necessary to effectively run a 2 on 1 break. Working it in the half court allows for more players to be involved and get more repetitions.
5 on 3 + 2 is a great drill to teach your basketball team how to take advantage of fast break opportunities where they have a numbers advantage, and then seamlessly move into your transition offense if you have not gotten the shot that you want.