I typically track fares on about a dozen trips at any given time. Does anyone have suggestions for tracking fares?

I use travelocity's fare tracker, but the e-mails are painfully slow at providing information about changing fares. FareTracker is a handy little program as well, but it sometimes has problems with a large number of trips (fares get all messed up). Also, it only visits one travel site. Any thoughts on SideStep? I used it once a long time ago, but it was riddled with spyware. Not sure if that is still the case.

Basically, I want the ability to track multiple trips and get fare updates daily (or even hourly ) and see the fares charted out over time, without having to go to sites and constantly type in dates and destinations.

One big problem I see with this is that all major travel booking sites (Expedia, Travelocity) prohibit automated means of obtaining search results or fares from their sites.

The author of any such tool would be a target for legal action.

That's probably the reason why the tool you mention only pulls data from one site - they most likely have permission to pull that data. Expedia and Travelocity are unlikely to grant such permission in my opinion.