We're a tiny business, and about 3 years ago we were looking for a good helpdesk system, and the one we finally decided to use is Support Center by qualityunit.com (http://www.qualityunit.com/supportcenter/). A gmail-like interface with email options, good tracking, and lots of nice features.

At the time, the single-agent version was free, and they still provided excellent support for it! We decided to purchase the unlimited agent version, even though we would have been fine with the free version.

It's a php/mysql system, and it's been very stable and easy to use for us.

They currently offer two options: a hosted helpdesk on their servers for $29/month, or a purchase option -- the price for the unlimited version is $199, and comes with 1000 days free updates and support. They may even run promotions from time to time...

Not free, but we've been VERY happy with the quality of the product and service they've provided to us.

(disclaimer: just a satisfied customer -- no other connections to them)