You need to try and keep the tool from getting in the way of working. In an ideal world the team will all be sat in a single room with big white boards, however often this is not the case and teams are distributed, or theres a push for some form of backup for the post-its.
I'm a big SharePoint fan and where you have this in house already, your already doing collaboration and team work on the platform. Adding another tool, with unique login's can work but the team need to really want to use them.
I've tried getting SharePoint out of the box to do what I wanted but it fell short. I've tried using Version One (on a number of occasions over many years, with many teams) but I find the tool is too much, there are too many otpions and things that need to be done that it gets in the way - it is a long way from the Whiteboard.
So I decided to develop what I needed for my projects. I needed a simple tool, and using the 37signals (creators of basecamp) approach I needed something with less features than the competition.
21Scrum is a simple scrum tool built on SharePoint that uses the platform, add the things that you need (white board, burndown charts) and leave you to get on with the project.
Perhaps this may be the best option for people who already have and use SharePoint - at least thats the goal.