VersionOne is a nice tool if you only have to manage one team across one main project. When you are an internal development shop and you have 30 people on about 50 different "projects" over the course of a year, it just isn't easy to reconcile them. We have some developers who fill a spot on three projects at a time and other projects that take 5 people full time for several months. It all looks good in the demo, but in practice it just isn't effective.
I have used Team System with Scrum, and it seemed to work fine, although I never tried the other systems.
We have been using TargetProcess for the past year or so and evaluated VersionOne as an option before we made our selection last year. Since then, both products have gone thru some pretty substantial updates.
My GENERAL thoughts about the overall philosophical differences that seem to drive each of these:
-VersionOne feels (to me) like a better fit for a more corporate environment; its reporting style, its (relative) rigidity seemed to me fit better in a company where the exact same process is followed on each and every project.
-TargetProcess feels (to me again) like its a better fit for those companies where the process is NOT the same on each project and sometimes you want to leverage one aspect of the system, sometimes others, and sometimes the whole enchilada.
We settled on TargetProcess for these reasons, not any one feature per-se as our business is a mix of consulting-ware style work and shrink-wrap software style projects that results in almost no two projects being ABLE to follow the exact same process.
I used version one about a year ago for a project and LOVED it. It has a very nice UI and is pretty easy to use. Plus, the follow what they preach...They are an agile shop with very frequent releases.
We are developing our own item templates in TFS
I have compared several APM tools in the past and found Target Process to be the best fit all around. It's organic nature and flexible web service API (NHibernate HQL sweet!) make it a perfect fit for teams that want to leverage an APM tool and integrate with other existing build processes. I find that their own iterative approach to delivering updates to the community allow users to take advantage of new enhancements rapidly, from quarter to quarter.
My two cents.
We're using ScrumWorks (the free edition) on two teams, 5 persons on each team. Works great for us, but we haven't tried anything else. Think we will evaluate VersionOne to check it out.
I didn't see anybody mention Rally Dev. I just saw a demo of that a couple of days ago and it looked pretty nice. Not as drag and drop oriented as V1, but lots of Agile-oriented functionality.
As for what I use (shameless plug), I use AccuRev on the SCM side for doing Agile development. :-)