My faves, in no special order.
-The Decepticon assault on Autobot City in TFTM, especially the brutal shuttle scene. The rest of the movie is pretty sweet too, but up until the end of Starscream's coronation is that much better IMO.
-There have been heaps of good action sequences in TFPrime.
-Pretty much any battle involving the Decepticons in Animated. Special mention to Lost and Found, A Bridge Too Close, and Transwarped.
-the battles in A Prime Problem were pretty good, as was the invasion of Washington DC in Atlantis Arise and the battles in Megatron's Master Plan Part 1.
-last ones off the top of my head, which I'm surprised haven't been mentioned yet: Beast Wars Code of Hero and, even better, The Agenda. The Agenda is easily my favourite TF episode arc/media of all time.