How I keep track of big story arcs varies depending on the situation.
If it's something I planned for going in, I've already roughly story-boarded out what adventures happen in what order and what the PCs should in theory accomplish in each one (see example below). Then, as things go along I keep rough notes which get refined each week into the game logs - one for me, and one online for everyone else. I also have to be aware of what story hooks are being followed up on and what ones are being ignored, so I don't waste time planning for something they've already turned away from.
However, if it's a bigger story that simply grows out of the adventures they do I'll dig back in the log and see what I can dredge up that might be relevant now, to make it all fit together better.
And on an even larger scale, I'll plot out strings of 3-5 adventures that can logically be tied into a single story arc (a good example is the 1e A-series) and then try to work out ways these strings can somehow fit in with each other; I'll also keep a list of one-off or diversion (or red herring) adventures to lob in if needed.
I also intentionally try not to let things get too complicated. If there's more than about half a dozen significant NPCs I have to keep track of at any given time (as opposed to NPCs that just lurk in the background until I need them) that's too complicated. City and-or kingly court adventures are horrible for this.
Example of an adventure-scale storyboard for my current campaign (that bears only passing resemblance to the way things actually went) in format "Adventure name - plot notes and hooks": (were I writing this on paper there'd be arrows leading from one adventure to the next)
1. Keep on the Borderlands - get 'em started, first contact with Ares cult, first contact with renegade Hobgoblins, first contact with monsters pouring into mountains, introduce politics and secret societies
2. Krykos the Warlord - small adventure, can be put anywhere, no real significance except to provide hooks to lead in to adv. #3 or #5 depending how things go
3. Shadowhaunt Temple - further contact with both Ares cult and renegade Hobgoblins, second time seeing them operating together should cause suspicion [if followed up, this leads to a 5-adventure arc]
4. Sphondalai Mountain Hop - party follow up and try to figure where all the monsters from adv. #1 are coming from [leads to a 3-adventure arc]
5. Defense of the Empire - party become agents working on behalf of a secret society whose goal is to reignite the fallen empire, the learn of the society and its fearsome (but decent) vampiric leader [could lead to all sorts of things]
As it turned out, they did adv's #1, 2 and 3; then one party went to work for the empire (giving a nice little story arc) while the other left-turned on me and decided to ignore the empire-rebuilders and may yet end up actively working against them; they ignored the mountains as well (a sub-party of quasi-retired PCs is just now dipping their toes into that mess), and none of them even bothered with the Ares-Hobgoblin business (which means it's still out there for future reference if I need it).
So now instead of working for their own empire they're mostly going up against another one (I'll get years of action out of this) except one party has gone a-wandering up north - their story really doesn't impact the main one at all...yet.
The advantage I've got - and the point I think I'm trying to make with all this rambling - is that the history and backstory are already in place and all I need to do is mine these for adventure ideas. Once that's done, keeping track is (or should be) relatively easy; but you have to keep some sort of a game log/story hour/whatever as that's the only way to remember details from one year to the next.
Lan-"of little brain tonight, it seems"-efan