I've used Minify with my jQuery/PHP projects with lots of success. It includes caching too so there isn't much overhead.
I ended up changing things around and using .htaccess to route all requests to my javascript folder to the minify script, so for example:
<script type="text/javascript" src="/js/jquery.js,js/jquery-levitip.js,js/jquery-facebox.js,js/datepicker.js,js/ga.js"></script>
with my front-end HTML routes into my minify script and it returns all those scripts as one, compressed and minified. That way I can define the includes normally and everything happens behind the scenes.
But anyway check the user guide on their site, it's very well documented, and you should be able to pull things off the way you want too. Oh and it works for CSS too.