In all three games, once I've unlocked the Random Stage Options menu, I've gone through and turned off the stages that were "not fun" to play on. In Melee, this included Icicle Mountain, Flat Zone, Brinstar Depths, and sometimes Big Blue and/or Poke Floats, depending on my mood. In general, stages where you had to focus less on fighting and more on not being randomly killed, were decidedly un-fun and I disabled them for random selection.
In Brawl, however, I really like the stages, and the vast majority of them are quite playable. So far I've only turned off 75m (because the platforms are not drop-through and you spend way too much time just trying to navigate the level) and Mushroomy Kingdom (because the Underground version leads to lots of scrolling death and not much Brawling). Even in the old Melee stages, Brawl has made changes that make them more fun:
1. In Yoshi's Island, they fixed the bug that made certain characters insta-kill themselves if they did a horizontal B attack over the three blocks in the middle. Ganondorf no longer needs to fear for his life on this level, and can concentrate on fighting rather than avoiding the three blocks of death.
2. Jungle Japes: With the addition of swimming, this level is suddenly way more fun! If you fall in the water, you don't sink; you can jump back out. However, I have slightly mixed feelings about this, because I am one of those sick *******s who actually loved this level in Melee precisely for the fact that it had some nice fighting platforms, and quick death to anyone who didn't stay on them...
3. Big Blue? I haven't played on it yet, but I suspect with Brawl's decreased landing lag before you can jump again, plus the wide assortment of characters with flying abilities, would make this level more fun.
I guess those are the main ones. In general, most of the levels in Brawl are fun to play on, have engaging (but not totally bat**** annoying) effects, and have pretty things to look at.
I do, however, miss many of the levels from the old SSB 64. Nothing will ever replace the old Mushroom Kingdom, with the warp pipes, and I will always have fond memories of Saffron City, Dream Land, and of course, Hyrule Castle, which was our group's official place for a grudge match.