What changes should be notated in a journal resubmission?
An editor once "requested" that I submit a "tracked changes" or latexdiff version of my resubmission if I wanted him to deal with it in a timely fashion. Since then, my strategy has been to submit:


revised manuscript (no annotation);
latexdiff of revisions against version submitted last time, to highlight every last comma changed;
cover letter, describing all scientific changes plus any major textual changes ("we substantially rewrote the methods section in an attempt to improve its clarity"). I refer the editor to the diff for minor textual corrections.


No editor has complained yet... ;)