[Amethyst]

Whether a cover letter helps or not varies, but if it's a decent letter, it won't hurt you. Someone who doesn't care about letters will just ignore it, but if you don't send one and that person likes them, it's a strike against you.

As for what it should contain, it's hard to say without knowing your field, but I wouldn't bother repeating what's in the resume. When I do them, I usually state the position I'm applying for and expand on a few parts of my experience that are most related to that particular position.

When I was hiring, I was more concerned with a bunch of short jobs (it made me worry the person was a flake and would leave as soon as he/she got settled) than a gap, as long as there was a good explanation. If you just can't find something, what about volunteering in something related to keep your knowledge up to date while searching?

Oh, and to add about references: I wouldn't bother checking a reference that was more than a year or two old. If you can find a way to keep involved with your field and have someone from that experience as a reference, even if he/she isn't a supervisor, that could be helpful.