Matt Raible has linked to some interesting resources that question the need for concatenating and minimizing js/css. With HTTP 1.0, it can be beneficial, but there are also downsides too.
For example, if you ship one large css file, a designer changes one colour, and that gets shipped. Now all users have to re-download the entire css file.
If you’re doing continuous, or even frequent delivery, your user’s won’t be able to cache the file.
There’s also an interview with an engineer from Google involved in the development of Chrome. In it, Ilya discusses some shortcomings of concatenating js, and also how HTTP 2.0 will hopefully address the issues.
Sounds like we’re nearing the time where structure of js/css will be more logical (hopefully yours already is), and they’ll be included in the page that way too.