>>1
A lot of the stores online have stocked up, so that they hopefully won't run out until after Christmas. I expect that they will have distribution deals in place for most of their newer titles, and some of the older ones, back in place by early next year.
That said. If you don't want to risk it (I didn't, either, and picked up a few shows, FWIW), I would recommend any of:
* Shakugan no Shana (not a box-set, just a bundle). This is, however, a title I would tend to expect someone else will pick up (there's still the unreleased OVA, the movie, and the upcoming second season, after all).
* Kamichu (a very nice box-set).
* Cardcaptor Sakura and the uncut/special editions of the CCS movies (not a box-set, but the second movie in particular has some nice extras). Geneon already dropped the license to the series (but not the movies), last winter, and I picked up the entire 18-disc (70 episode) bundle for ~$140 - it can still be had for about that much.
* Tenchi Muyo OVAs (box-set). Old enough that it may not get picked up, unless FUNi (who have the third OVA) decide they want it.
* R.O.D. the TV (box-set, but over-priced). I've held off on buying this for nearly three years, because of the price (around $170 for a 26-episode series). It's a bit of a niche title, though, and this may be the last chance.