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 install.php into wp-content directory.
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.