I have long been of the opinion that Dungeon adventures on average are a whole lot better than even some of the classic official moduels TSR put out over the years. The format allowed for intriguing adventure ideas to be pursued that would not have been a big -seller in module format - but was great none-the-less - esp. non-dungeon crawl type adventures.
You're preaching to the choir.
Every time people ask for "best module?" and start talking about official 1E module X or 2E mega-adventure boxed set Y as being the cat's pajamas or "best of all time", I'm tempted to suggest that they get Dungeon back issues instead, because every issue seems to contain something better than the majority of official modules out there.
It's inevitable really; who's more likely to produce the higher quality adventures in the long term - a handful of designers with deadlines, or hundreds or thousands of gamers worldwide with no deadlines teamed with a ruthless editor?
But I run an "organic" story/character-based game - I use Dungeon Magazine in a "mosaic" style - snipping togther bits of adventure or changing elements to fit them together - sometimes I doubt the authors of said adventures would even recognize them.
Yep - there is even less excuse for not doing such customisation these days because if you're using older issues you need to get your hands dirty converting it to 3E anyway, so why not remix them to your needs whilst doing so?
Some other observations on using Dungeon magazine adventures in campaigns...
Condensation of villains and towns seems to be necessary, since they seem to present a new one of each every second adventure. Dungeon is an excellent source of town locations because they keep reinventing the wheel with bits of a new village to save all the time. It presents and interesting quandary, IMO, as well - there are a large number of "help or save the town" adventures over the years, but if you condense them into being about the same few towns, how many times can the players save or help town X before they wonder why they're bothering? As a plot hook it seems to be worn out, but can usually be switched with something else (such as an NPC under threat).
I also find that most Dungeon authors, just like most official module writers, don't write dungeons to my taste - generally too focused on the realism side things, what I consider "barracks, beds and boredom". I prefer the "adventurer obstacle course" approach of magical traps, puzzles and interesting curiousities, ala White Plume Mountain or Undermountain. I am, however, clearly in the minority given the number of people so concerned about how monsters get their food rather than whether their dungeon is much fun. I'm being facetious, though; verisimilitude certainly adds to fun, and is an admirable pursuit. Best case scenario is achieving both, I suppose.
Another thing I have observed is that some Dungeon plots never make much sense from the players' perspective; the intricate events that set up the adventure are hidden away in the DM's Background, and justify proceedings from the DM's perspective but not from the players', because they never find out this stuff. More than one seem to need alteration in this respect as well - so that they make sense to the PCs.
A final observation I think is "seeding" the campaign setting with the adventures you plan to run ahead of time. If you plan on running Secrets of the Towers later in the campaign, make sure that the towers are already there from the start - maybe the PCs have even heard about them - from the start. Same goes for McGuffin NPCs and villains - they shouldn't just pop up when you're going to run the adventure. The danger is that the PCs get interested in these locations and characters at low level and raid the vampire lord mayor's manor, in which case you have the options of either staving them off somehow, letting them run into tough encounters and take the hint, or converting the adventure or location downwards in level...
As for how I run my game - all I can say is, obviously you never read my story hour
Heh. I'll check it out...