Looking at the codex, and searching here, I can't see any reason why excluding categories from the loop like this:
if (in_category('39') ) continue
wouldn't work. But it doesn't seem to.
The old Ryan plug "front page categories" which I've relied upon for so long doesn't work anymore in 2.3
How do you exclude more than one category (ex: 39, 40, 41, 42) from the index (home) now?