My first thought was the BackupBuddy plugin from iThemes. The downside is that it is very definitely not free. Actually, the code is all GPLv2, but you can’t get it unless someone who has paid for it (like myself) gave it to you (which I’m not offering to do for ethical reasons).
However, the basics of what they are doing is not Rocket Surgery®. Basically you setup a WP install to be whatever you want your “custom install” to be, backup both the DB and all of the files, and then move those to wherever you want to do the install. The iThemes plugin is slick in that it handles rewriting all of the embedded urls in the DB, but that’s pretty straightforward. Then there’s a few values in wp-config.php you need to tweak, but again, it’s not that difficult.
I’m doing something along this line because I’ve gotten tired of always installing the same set of must-have plugins. I also like having a bunch of Lorem Ipsum pages so people aren’t dealing with quite so much of a blank-site.