Piratecat from reading your ongoing plot and how your weaving a fun story I wonder with your multiple year campaigns. Do you stick with a single story arc the whole way through, or is it less the campaign is the story arc and more simply the stories the PCs get involved in.
When I first started my 16 year long Defenders of Daybreak game, I'd say the first 2-3 years were just running adventures from Dungeon Magazine and finding ways to link them together. Slowly this made me think about how bad guys might be linked. I always avoided big overarching plots; I finally tried one about five years in, and embarrassingly a plot I thought was going to take six months took 18 months instead. Ridiculously fun, though.
So I started thinking about other big plot arcs. I never planned too far ahead; I'm one of those DMs who have far more fun when the players surprise them, and a lot of my game sort of accretes based on what the PCs accomplish or kill.
The trick for me is not to use one giant plot arc. I think that gets boring and really one-dimensional. Instead, it's a little like jazz: you have a theme, and lots of variations around that theme, and sometimes the music wanders off and gets totally distracted for a while before it returns to the main tune. So you want to have a mixture of big-plot-related adventures and completely extraneous adventures, including some that are simply just fun to play. Making sure that you have a variety of emotions - joy and easy kills and hard kills and despair and oh crap we're all gonna die and whee treasure bath! - helps keep the game feeling fresh.
In my current campaigns, each of the two groups have a vague plot arc that I know about. In some of their adventures they're seeing the echoes of that plot trickling down to them at 2nd-3rd level. I don't like hitting players over the head with the plot-stick, though, so I throw out about four times more plot threads than I need, and follow up the ones that the PCs bite at.
You expressed some concerns about one adventure messing up the feel and themes from the last. Don't be afraid of this, embrace it - it's a good thing. Think about how Buffy the Vampire Slayer or X-Files handled their seasons: some shows were about the overall plot, and some were self-contained episodes that were unrelated, but even these kept the same continuity (hopefully). The funny episodes were a welcome respite from the scary or tense episodes. By making people laugh, they make scary episodes more disturbing in comparison. D&D is exactly the same way. If I tried to keep a mood (especially a dark and oppressive theme) up all the time my players would revolt and go play Paranoia instead.
To get back on topic, my current campaigns will be 6 years each (leveling 5 times a year, once every 5 sessions) because I realized that if I keep running 15+ year campaigns, I'll never have more than another two or three before I kick off from old age.
