I ran into a little trouble with the annotate module, and had a look in the source.
It appears that using the settings I had (which were pretty much default) it would
not work...

I had my cvsroot set to /home/cvs, and was doing an annotate on a script that I had
in my scripts module, and was getting exceptions about the root being wrong. It
turned out that there was an extra '/' going into the path, so it ended up trying to
look at /home/cvs//scripts/blah... The offending line was:
$fl = new CVSLib_File($CVS, $CVS->cvsRoot() . '/' . $where);
it turns out that $where is "/scripts/blah...", so obviously the fix for me was:
$fl = new CVSLib_File($CVS, $CVS->cvsRoot() . $where);
(line 20 of annotate.php)

Obviously this will still have problems if I was to change my cvsroot to /home/cvs/,
but I figure that these types of cases will be looked after further down the
development path :) I would fix that, but I don't really know php... I am looking
at learning it, but not in the next few weeks at least, so I thought if I let you
know this now, then I won't forget :)