Our team does both new project work as well as ongoing work like bug fixing etc. I am looking for ways to track them separately so as to distinguish new projects from ongoing ones.
I always seem to find my way back to JIRA. You can customize an issues workflow for specific projects, or even issues types. This allow you to handle bugs differently than lets say tasks or features for a new project. The GreenHopper plugin is also quite nice if you are working on a Kanban or Scrum team.
Use project management software or an excel spreadsheet, as opposed to bug tracking software. Create categories for the work that you are doing e.g. Bug Fixes vs New Development.
I'm curious as to why you'd want to track them separately. Both "types" of projects require management, it's just that the tasks being done are slightly different as the lifecycle goes on. Management gets a little more difficult when the tasks are popping up in an ad-hoc manner (bug reports), rather than having a large net of tasks that are all defined and just need to be done, but the difference is more in managing expectations rather than managing the prioritisation and assignment of tasks.
What is it that you track, and which aspects do you want to track separately? If you tell us what's not working for you right now, you may get more responses.
You can try Team Task Manager. We use it daily to track projects and tasks, it's very intuitive and there is no learning curve. Free eval is here - http://www.deskshare.com/team-task-management.aspx