I've just upgraded to 4.2 (nice, btw, almost flawless process)...
On my project list is to go through my templates and try to streamline things a bit, a part of which process is to comb through my stylesheet and ditch what I can of stuff that's left in there since like 2.x and no longer in use.
On a global search (BTW, under 4.1 the global template search would always 500 error, now it works) for "banner-commentspop", for instance (which I assume used to be used in the comment and trackback pop-up window that is no longer in use) I have found it located in a whole bunch of old templates on several blog: TrackBack Listing Template, Comment Listing Template, Comment Error Template, Comment Pending Template.
Thing is, though, that when I look at the template lists for these blogs, these templates are not listed. They can only be accessed through the search screen.
I assume these are old system templates or something that are no longer in use but that the system has changed so as to make them inaccessible or something, and that the search engine is actually coming up with. Something like that maybe? Think I'm safe to check them all off and delete?
Reported on Movable Type 4.2
You should have an option called "refresh templates." Just run that, tell it to delete the old templates, and it should reset your templates database tables for that particular view (system or blog) to the new default. Of course, if you do that, you'll lose any changes you wrote into them.