One thing I really miss from managing my Git repository in IntelliJ is change lists (http://www.jetbrains.com/idea/webhelp/changelist.html) which are essentially grouped changes.

They are very handy when a developer has several things going on at once (e.g. your core work and some comment cleanup) that they want to keep separate. I find them incredibly useful.

In SourceTree I envision something as simple as "by groups view" that groups the hunks in the working tree files - essentially a one-level tree view. The user can drag between groups like they can for staged/working. There would be an ungrouped group and the ability to add/delete new groups.

Commit would work the same as now, you stage what you want and commit. You would, of course, be able to stage an entire group.