These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Ultra Magnus was locked up in his universe for trying to usurp Optimus (and he got his face ripped off in addition to failing). He and several others travel to earth, where he assimilates numerous Autobots into the Junkion hordes (becoming mindless slaves and dead in all but name). After that, he proceeds to set up a plan to take rarified energon from earth with his sword and destroy it. His plan is foiled when a shield is placed around the earth but his real plan was to actually cause the death of the entire universe! He just destroyed a reality! Even the Normal Decepticons turned against him (They wanted to be the conquerors) and were appalled when they realized the extent of the damage.
Thanks to his Ascended Meme status and general adorableness, Ravage gained a lot of fans. Pictures of him waving with variations on his Catch Phrase "Can U C me totally waving @ U!!!!!!" are common, and often even people who don't know much about the rest of the continuity will still know all about him, despite him being a very minor character in the actual plot.
First Installment Wins: Since the original comic is (so far) the only story available outside the fanclub, not only is it the only part of the universe most people know, but many folks also don't even know there were more stories.
Ho Yay: Starscream's behavior around Megatron tends to vacillate between "fussing mother hen" and "teenage schoolgirl with a crush".