My recommendation is to actually build your own out. I work for a shop that does about 20-30 custom themes a year, with all of them having real similar functionality, but usually isn't standard / common in most themes.
Then, whenever a new theme needs to be developed, we basically copy / paste this default set of template files into a new theme folder on the WordPress install. For us, items we've included in this default setup are pre-populated header.php, footer.php, index.php, home.php, single.php, functions.php, comments.php, /images (dir), /functions (dir), style.css, /css (dir), /scripts (dir), and a handfull of other items.
Then we've also used Yahoo Grids, 960 or Google Blueprint css frames works to also speed up the css work. There's a few other items / files I'm leaving out, but should give you a general idea of what works best for us in our shop.