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Mine is a four way tie between Megatrons reformatting, Dinbots attacking Devastator, Starscreams death and Unicrons transformation

Wreck-gar's attack on the Autobots at the Junk Planet, with awesome Weird Al music backing the scene.

Starscream chasing the autobots into the transforming city, and having to shoot his own foot to escape getting crushed.

The whole attack on the city is a big fav of mine. Particular parts of it that stand out, Hotrod firing on the shuttle, and Dinobots vs. Devastator.

Starscream's coronation, Hotrod & Kup vs. the Sharkticons, and Dinobots vs. Unicron are also favorites.

when prime jets up, transforming in mid-air and pwning half a dozen decepticons.

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The entire 1st part of the movie up to Prime's exit/Megatron's reformatting.

Optimus' fight with Megs.