In the past I've had success in making custom WP installations using custom
install.php file. I remember I mostly followed this tutorial and improvised:
Automating WordPress customizations – the install.php way @ WordPress Bits
The trick was in overriding the installation process by putting your own
Note that both articles are from 2007. It worked for me in the past but I'm totally not sure if this method works now with WP 3.3.
Presently I just use a custom bash script to do a quick install with my favorite plugins and a small plugin to loop through the settings I'd always used to change. I can share a code of both if needed but I believe much better scripts for both can be found online.
While I was searching for the above tutorial I've found
WPkgr: WordPress Custom Install PKGs -
I've never heard about it nor tested it but it looks like worth a try.