B.L.U.F. — You can pick your favorite timer app, and use the Afloat app. It's a tool that allows you to keep any window on top of others. You need to install SIMBL first to use Afloat. More info in this article.
DEETS — I know its been years, but I would benefit from this as someone with adult A.D.D. as the in-your-face countdown for what I'm supposed to be working on. I tested 8 different timer apps avail in the app store, but non stayed on top... well, one did, but it was enormous and I wanted something small (because the big one was distracting and, again, A.D.D.).