I still remember the gut wrenching feeling in my stomach watching in horror as smoke poured out of Prowl's mouth as he went down. At the same time I thought the way they played it to Instruments of Destruction made it very cool.
That scene alone pretty much ended Transformers for me (at least until the 1st live action movie)....not that you would get that idea from my screen name or anything.
I'm glad you mentioned "Instruments of Destruction" because:
I hated the 86 film with a fury of a 1000 burning stars, so that automatically anything in that doesn't get my vote.(I think its meh now days but you'll never hear me say I like it.) It's music is pure cheese, which if you didn't grow up in the 80s, its pure fail.
I felt that way about the film, but now it's more of a 2 parts dislike for it, 1 and a half part appreciation for its boldness and a few great scenes. However, and as somebody with no appreication for that 80s hair/jock rock niche, I must say that the music in the film is probably its highlight. Taken alone, the music is probably laughable; in the context of the movie and how certain parts of the music are punctuated by the action on-screen, it somehow is deserving of most of the praise it gets. I particularly like how the music never stops throughout the movie, its non-repetitive breathless pace topping that of a plot that stalls around about the time the 2 Autobot shuttles of characters I would rather forget get shot down.
I can go into a drawn-out diatribe about the weakness of the '86 movie, but I'll attempt to sum it up in a neat package: beloved old characters were replaced with lousy new ones in almost no time at all. So many new characters and concepts(Matrix? Junkion raves?) are thrown at us in such a short amount of time, that even the most well-versed of TF fan at the time must have wondered just what the hell happened.
Worse, the rules of the game changed as the action went on. 1 single shot now sends an Autobot to his manufacturer in the sky, but Ultra Magnus is blown apart, only to be put together by Wreck-Gar glue a few minutes later. You then realize that if a character was introduced 15 minutes ago, he's going to be surviving no matter what. So much for the "immediacy of death" you just experienced on the Autobot shuttle 5 minutes into the film.
However, there are a few great scenes in that movie with impeccable animation:
1) The "inside Blitzwing" point of view when he is taking aim at Hot Rod.
2) The "inside Hot Rod" point of view as he runs over Galvatron...I particularly like how you see the steering wheel turning with Hot Rod's movements.
3) Devastator crushing through Autobot city after Megatron's line of "Let the slaughter begin!"
4) "Megatron must be stopped. No matter the cost"
5) The Sharkticon's teeth falling out after getting punched.
6) Hot Rod's inability to decide on a single transformation.
7)The inner workings of Megatron getting overhauled into Galvatron.

Thundercracker clearly being present at Starscream's coronation after he was just turned into Scourge. Same with Shrapnel on the planet Junk (gotta love those animation errors in a big budget production).