Earlier quoted context omitted.
I say yes. I like to keep information about the code as close to the code as possible. Issue trackers come and go, and even if you keep the same issue tracker around, how are you going to relate the change in the code to the particular issue down the road? FWIW, I also prefer READMEs to Wikis.
> Issue trackers come and go What do you mean? Just put an issue ID in the code and/or commit.
Referring to the issue ID in the commit message is a fine practice in addition to writing good, comprehensive commit messages. Commit messages that consists only of an issue ID are – in my experience – utterly frustrating to deal with. They tell you nothing more than this change is somehow related to this or that bug or feature, but not how or why.