I'm running a game with a lot of players, and on any given night there may be a different combination of them. I like it a lot, and it helps the covenant feel large and rich with a diverse kind of stories. However, keeping up with plot hooks and the progress of plots is starting to be difficult for me as it turns into a massive web of intrigues (which is what I'm going for!)
Since it has a lot of the same properties of the Vampire LARPs I used to play, I am currently using grapevine as a program to keep up with rumors, who knows what and who is doing what, but that program is well designed for White Wolf WoD.
Is there a similar open source (or inexpensive) program that would serve me better?
I swear by Scrivener (literatureandlatte.com). It's what I'm using for NaNoWriMo again this year. It's flexible enough that you can organise yourself pretty much any way you want to with the bonus that you can compile your notes to a number of useful formats.
Also, I've just invested in Aeon Timeline (scribblecode.com), which is great for getting your timelines right, either retrospectively, as you track your saga, or for when you plan those events yet to come. You can create "actors" and "events" and break those events down by story arc, even associating the actors with the events. Again, it's quite flexible and I'm actually using it at the moment to try to keep track of all the ideas I have floating around and place them on a timeline so I know when I should get to them.
Both of those have free trials and they're available for both Windows and Mac. Worth giving a go.
It isn't open source or freeware, but Realmworks from Lone Wolf Studios is exactly what you're looking for (and awesome, but I've been a beta tester).