I didn't really start to watch John Hughes movies until after he died, believe it or not. They'd just never come up until then, but the following year there was a seven movie marathon at the Castro, so I took the opportunity to play some catch up. I actually rather liked them, teen soap operaness and all. There's a mark of solid sincerity about them, especially in Sixteen Candles and Some Kind of Wonderful (my favorite of his teen movies), and I think they work even past the shmaltz. Also, Breakfast Club is one of the few movies that can get me from laughing to tears and back to laughing in a single five minute span (The indisputable Anthony Michal Hall's confession), so points to it for that. For all their now-apparent flaws (and the fact that they're all upper class WASPs, except when they're not), all the kids have a good, real feeling to them that makes it all sink in better. All that said, I do admit I prefer his adult stuff best, so that's Vacation and PTaA (and Uncle Buck! We must never forget Uncle Buck, for it is amazing).
Meanwhile, I will also admit that Blazing Saddles is the more quotable of Brooks' films (well, not always in polite company, at least), but I still love Spaceballs. Loved it when I was young, loved it now. It's more lowbrow humor, but a lot of it really works. Especially the little things, like John Hurt's exasperated reaction to getting chestbursted again.
Clue was a random Blockbuster rental when I was a kid, back when I was more amazed that such a movie existed and before I would've been suspect about such a thing. Luckily the movie turned out to be hysterical, and I love it to this day. I will say that, considering the caliber of the talent involved, it probably could've stood to be better, but as even Johnny pointed out, they've got such a wonderfully manic energy going that I can't help but laugh. Also, the singing telegram bit is aces. Always has been, always will be, if you think otherwise there's something wrong with you.
Finally, I need to plant myself firmly in the "Full respect" camp for They Live. It was restricted by its budget in the third act, and spends a bit too much time trying to be a cheesy action movie, but the ideas its throwing around are quite fascinating and always relevant. That the latter is true is somewhat depressing all these decades later, but what are you gonna do (shotgun killing sprees aside).