For me:

1. War For Cybertron (PC) - Finished and loved, tempted to play through again!
2. Transformers: Armada (PS2) - I loved that game but was never able to finish it as I lent it to a School friend who moved to Queensland.
3. WFC Autobot/Decepticon (DS) - Easily the best TF game on a handheld to date but F@#$ me are the time-limit stages ridiculous!
3.5. Beast Wars (PC) - Why?, PC is best and it indeed used to use the mouse 1AZRAEL1, but alas I only ever had the demo and I've not been able to get a downloaded Full Release version to run properly on modern hardware... yet!