i have recently shifted from Mantis to Flyspray for issue tracking.
I have been using Mantis for over a year now and its a very comprehensive bug tracker with a lot of features. The UI is a little dated though. One of my main problems was that the UI became a little slow in loading once the number of bugs reached around a 100. I suspect the database retrieval code was taking too long to fetch data so the page would load halfway and then wait for a couple of seconds before it completed the page load. Perhaps it would run better on a dedicated server. For the above reason, I was looking around for a more leaner and meaner software. The little drawbacks notwithstanding, Mantis remains a very good choice for large teams with multiple projects.
Flyspray has a very fast and clean interface. It’s screens do not have too much of data and the look is slick. I find it more easier to use than Mantis mainly because it requires less data than Mantis. Flyspray does not allow for too much elaboration of bugs, but it does deliver the goods for a basic bug tracker. It’s setup screens are one of the most user-friendly I have seen for any web application. Strongly recommended for small to medium sized projects.