Scott Taylor

Similar to what we use on eMusic – this software is still experimental, but take a look!
Automagically concatenates JS and CSS files that are output in wp_head() and wp_footer() – stores / serves them from Memcached (if installed) or Database. In a load-balanced environment, the generation of flat files can be expensive and hard to distribute. Minify takes advantage of Memcached and Site Options / Transients to do the work once and share it among all servers in your cluster. File names are dynamically-generated to allow cache-busting of a CDN like Akamai that doesn’t always cache-bust by query string.
New .htaccess rule! 
 RewriteRule ^([_0-9a-zA-Z-]+)?/?wp-content/cache/minify-(.+)-(.*).(css|js)$ /wp-content/plugins/minify/make.php?hash=$2&type=$4&incr=$3&site=$1 [L]

Minify

Automagically concatenates JS and CSS files that are output in wp_head() and wp_footer()

Motekar

Upload files to custom directory in WordPress Media Library.

Custom Upload Folder

Upload files to custom directory in WordPress Media Library.

Minify vs Custom Upload Folder