You already seem to have a .Net thing under control - so here's the Java perspective.
We used Jira forever, and since the advent of Scrum, we started using a plugin called Greenhopper , which makes Jira more friendly to battle. It allows you to create stories, errors, etc., Post them on a virtual storyboard, and if you understand that everything is in order, it will generate your burnout graphs, etc. We have one team with developers, distributed in three different cities, and online storyboard works well for them.
EDIT: I have to clarify that teams that are all in one place more often use posts and boards, and Jira less - but there is a traceability element that brings Jira that I like, so I always try to push someone to keep Jira in current status.
For continuous integration, we use Hudson, which will control version control and builds using one of our two build scripting tools - Ant and Maven . There are many functions offered by Maven and its various plugins, it can be made to work with different application servers, maintain the repository of your Java libraries, etc. Too much for one answer :).
Hudson can be connected to Jira, so when the developer comments on the code, he will watch version control comments and if he sees something like a Jira problem number (for example, PROJ-293), he will put your version of the control comment on the problem in Jira , as well as the state of the assembly, which turned out to be stable, unstable, broken, etc. I know that this works with Subversion, which we use, I can not comment on more fashionable version control software like Git, Mercury, etc.