I've started using IntelliJ change sets, another great feature. A change set is very intuitive: a set of related changes. Typically the changes are related to a bug.
IntelliJ tracks those changes as a group: all the changed, added and deleted files. You can then commit those changes as a group, without checking in anything else.
This is just perfect for checking in a quick bug fix in the middle of a larger body of work.
Nice features: You create a comment when you first create the change set, this comment is the default check-in comment when you do commit changes. Further, they didn't skimp ... you can move a change between change sets.
The pattern I'm seeing is that IntellJ has features that cover specific things I've had to do manually and awkwardly in Eclipse. I can definitely remember times I've fixed a small bug and had to carefully pick and choose which files to check in, because I had many unfinished outstanding changes waiting to go. IntelliJ just picks up the slack and does it for me.
I'm not sure how you handle this situation in Mylyn, Eclipse's super-invasive ... tool? Framework? Filter? Nanny? Whatever it is, I guess it can do it, but I doubt it accomplishes the same goal as simply and comprehensibly.