I need a tool which can minify, optimize and munge many files of those possible types
The final result should be one HTML file only with all JavaScript and CSS embedded or in the worst scenario 3 files respectively for HTML, JS, and CSS.
I am aware of tools like YUI Compressor etc. What I currently have not found is the type of compressor which will work on all those file types and merge them in one huge file only.
Gad, consider the drawbacks to minifying CSS. If you don't have a system where you edit normal/minify/ then deploy it can make later editing of CSS rather dicey.
I went through this whole argument on a big UI refresh project for an international bank. One site in particular was doing 1million+ visitors/day and bandwidth numbers were insane despite all our efforts to keep it minimal (every little bit adds up on a site that heavily trafficked) Upon business analysis by a large team of very talented minds, it was determined that we would take several steps, but NOT css minifying due to the added time it would take engineers to undo the minifying before fixing, minifying and redeploying for simple CSS tweaks. The numbers showed that even with a 5gb/day bandwidth improvement, it was still cheaper to not pay a UI engineer for the extra time.
We don't know your site's specifics, but there aren't terribly many that have to worry about the traffic my example uses. Run your site in Firebug's new speed analyzer and see what the real benefit could be from minifying.....now multiply that by your traffic. Usually, that number isn't too scary. Spend your time doing image sprites, combining css and js into respective files (better than mashing into individual php files due to caching benefits) to limit http requests, and ensuring that caching is properly setup. Run gzip compression. If after those steps you're not good, then take the site to a new level.
Keep it simple....it makes a huge difference in the update and maintenance portions of the site's lifecycle. With the time and headache saved, you can help us out with our questions :)