Here's a few I liked:
Issue #54, "Unhallowed Ground." Sorta-kinda reminds me of "The Name of the Rose" (murder mystery in a monastery).
Issue #61, "To Save a Forest." Fun wilderness adventure. Nice change from dungeons & ruins.
Issue #63, "Hunt for a Hierophant." Another wilderness adventure, though it wraps up in a dungeon. Can work as a follow-up to "To Save a Forest."
Also, "Invisible Stalker" is a nice Side Trek adventure. City adventure that could be good to fill space, kick off an adventure, or use to introduce a plot hook.
Issue #72, "Plundering Poppof." Another low-level city adventure that you could link to "Invisible Stalker" somehow (if you wanted). Interesting puppet.
Issue #76, "Mertylmane's Road." Good arctic adventure that has the heroes fight off the advance forces of an enemy army.
Issue #78, "The Winter Tapestry." Another arctic adventure than can be linked to "Mertylmane's Road" if so desired.
Don't have very many old issues of Dungeon--I'm sure there's some classics that some folks may be able to point out to you.