The fastest and most straightforward way of merging them (without hand-coding, testing and so forth) is to use a minification plugin. These not only strip out unneeded characters and comments from the files, they also combine them into a single file for you.
I've used wp-minify with good success, and it is fairly easy to use. It is also lightweight. You'll notice your site speed up almost instantly. http://wordpress.org/extend/plugins/wp-minify/
Another good plugin that will handle this for you is W3 Total Cache. This is a larger, more comprehensive performance enhancement plugin. Minification is only one of its modules. Using W3 to minify gives you more options and you can do things like control the order of the files to resolves conflicts. This is a complex plugin and there is a learning curve to set it up, but it is generally worth the effort.
What you are undertaking is a fairly common but sometimes time-consuming process to get right. The biggest issue is understanding how to resolve conflicts.