Oh man, so many.
Tabaxi have been a mainstay of my campaign since 2e, and I don't believe they've ever made a MM1. The avolakia from 3e's MM2 are amazing. Most of the not-MM1 demons, devils, and yugoloths are awesome. The aurumovorax. The son/spawn of Kyuss. Death knights (though they're in 5e's MM1!). Wrackspawn from 4e (first in 3e, yeah yeah, but they got a really cool update and great lore in their Torog connection.)
There are just so many cool non-MM1 monsters in every edition!
So to organize a bit by edition/book- and this is just off the top of my head:
1e- Fiend Folio: Tabaxi, death knight, slaadi, daemons, lizard kings, lamia nobles, sons of Kyuss, apparitions, astral stalkers, oriental dragons, carbuncles, al-mi'raj, algoids, aleax, svirfneblin...
1e- MM2: gloomwings, tenebrous worms, stegocentipedes, afanc, aboleths, bigger vermin (megalocentipedes), quicklings, fomorians, myconids, cloud dragons, shadow dragons....
2e- various MC appendices and the like: dharculus, demons and devils (by whatever name), many dragons, beholder kin, illithid kin, etc. Hard to remember what was in what since I put them all in the same set of binders.
3e- MM2: Gravorg, avolakia, death knight, mountain giant, etc.
3e- FF: ulgurstasta, various fiends, hullathoin, grafts and symbionts (!), more inevitables, etc.
3e- MM3-5: Lots of cool but not very developed things. Harpoon spider, the proto-foulspawn, tirbani, the name escapes me- the blue centaurish like things that bellow and bully, etc.
4e- Generally, the later the book the better the monster design. Banderhobbs, various awesome composite elementals, fell taints (evil flumphs!), pod demons, osteopedes, various dragons from Draconomicon, etc.
Also, let's not forget monsters from adventures or other weird sources- for instance, the steel predator (3e) is great, as is the chagmat (1e).
Man! So many.