Once again a stupendous issue - and very much on the cutting edge of what is happening in the Development world.
Liz, you briefly mention "companies like VA Software and CollabNet bring collaboration and development tools from the open source community into commercial environments" - as both a business woman and an open source user I understand the need for a blend - open source and/or low cost!
Just wanted to mention a fantastic company from down under - Atlassian - they offer an excellent project/bug tracking and a phenomenal wiki tool at an extremely low cost. We recently purchased both products and have been very impressed with their own "rapid development" techniques and responsiveness to user feedback and requests.
It would seem that this type of middle ground would be an entirely acceptable means of direction in which to move. It has been for us - and we are an educational development organization - so you can imagine our budget!!