Yes, of course we should use a seperate CSS file for printing. Also, we can use Syntax Highlighting Plugins for showing the code nicely on website. You can have a look at the following options.

Free Syntax Highlighting Class Developed with MooTools
Syntax Highlighter Helps Posting Code Snippets Online

Then printing might become an issue, but one can easily use a different css for printing pages with code.

I’m curious as to what you think is the best method to do this.