I would agree with adding bugfix ids in commitscommit messages, and not within the code itself. Bug trackers that automatically scrape commit messages for bug ids are very useful.
In addition, you can use the blame/annotate/praise command of your version control system to help replace these comments. Then, when you run something like:
vcs blame file.ext you can see useful information, usually including who changed each line, when they changed it, and the commit id. From the commit id, you can get the full message, which should include the bug id.
Good VCS systems will let you ignore whitespace when calculating who modified a line.
I don't know what Clear Case has for this feature.