The ones with the Creature Catalog inserts (I-III, issues 89, 94 and 101). They can be pulled out like the modules, and are like mini-monster manuals, and the artwork is good. IIRC, one of them (II?) is also missing from the Dragon Magazine archive. I don't have these issues anymore, but I still have the Creature Catalogs.

I didnt start reading Dragon until after #50.  So most of my favorite issues are between #50 - #100.

Issue #64 featured Assassins & the Assassin's Guild.  It had a mini-adventure/proving ground called The Assassin's Run.  It also contained a game by Tom Wham and Jim Ward called Planet Busters.

Issue #67 contains the awesome Astral plane adventure Fedifensor and an entire chunk of the issue is devoted to the Astral plane.

Issue #74 contains the Dragon Magazine Combat Computer.

Issues #75 and #76 have Ed Greenwood's fantastic articles on the Nine Hells.  #76 also has the Deathmaster NPC class (which I always thought was corny but awesome at the same time).

Issue #81 has the adventure The Ruins of Andril.  I do believe one of my characters died in that one.

Issue #83 contains the adventure The Dancing Hut.  Baba Yaga's magical abode.

Issue #86 had the do-it-yourself castle named Big Stoney.  Did anyone actually put it together?

Issue #100 had two great additions:  The adventure The City Beyond the Gate and Dragonchess.

As far as Dungeon magazine is concerned, most of them have at least one good adventure but the ones that really stand out (at least for me) are:

#20 for the adventure Ancient Blood.  Vikings and giants.  'Nuff said.
#37 for The Mud Sorcerer's Tomb.  Think Tomb of Horrors lite.
And issue #70 for Wolfgang Baur's most excellent adventure Kingdom of the Ghouls.

There are (arguably) good quality issues past the 50s and 60s.  But for value, it's probably a short list - mainly those with some sort of insert that was often removed/lost.