A quick Google search turns up quite a few interesting discussions around this topic on StackOverflow.
One of the more interesting suggestions to emerge from reading these, was to use Google's Closure compiler for this purpose.
From the Closure compiler's documentation:
Compilation with ADVANCED_OPTIMIZATIONS removes code that is provably unreachable. This is especially useful in combination with large libraries. If you use only a few functions from a large library file, the compiler can remove everything except those functions from its output.
Regarding, the removal of individual files, as felgall points out, the browser will have cached them anyway, so this makes little difference to your overal performance.
However, I just had a look at your site and have a couple of suggestions/observations:
- You would do yourself a favour by using the minified CSS and JS files that come with bootstrap. Bootstrap now comes with just one minified JS file which will save you several HTTP requests and a few kbs.
- You might want to take a look at customizing your bootstrap files. Here you can get a good overview of everything that is bundled with Bootstrap and deselect (i.e. not download) the components you know that you don't need.
- If you want to optimize your site's performance, then you might consider using Google's [PageSpeed, or Yahoo's [URL="http://yslow.org/"]YSLOW (see [URL="http://net.tutsplus.com/tutorials/other/speeding-up-websites-with-yslow/"]here for a tutorial](https://developers.google.com/speed/pagespeed/)).
Hope that helps