Hmm... I can't decide between all of MTMTE, all of TAAO or all of ex-RiD
All are incredible stories in their own right in their own way that really raised the bar on what we can do with storytelling in this franchise. ... Well, arguably, LSotW and Chaos Theory done that first but these REALLY pushed it.
So instead I'll just pick some favourites from other corners of the franchise
Gone but not Forgotten - Marvel US.
Particularly US because Furman **** itDeadlock - Transformers Prime. Just a really great finale with great fight choreography
Deadly Aim - TFCC Of Masters and Mayhem. Though really, all of OMaM is fantastic.
Code of Hero / Transmutate - Beast Wars. Once again, brilliant stories that really pushed the bar on the sort of storytelling we can do with Transformers.
All of Transformers Animated. Best Transformers cartoon we've ever gotten.