One of the things I’d really like to see come to Evernote is built-in syntax highlighting, which is something I bet a lot of developers would probably like to see. Until that day comes I will have to stick to online syntax highlighters that take my code and turn it into something that looks a little prettier. I can then copy their output, and since Evernote supports the rich text I can simply paste it into a note and the syntax highlighting style will be retained.
One of my favorite online syntax highlighters is Quick Highlighter. You just paste in your code, select the options you want such as line numbers, and the end result is some heavily beautified code. One of my favorite features with this particular syntax highlighter is that it can identify built-in functions, and at least with PHP it then hyperlinks to the appropriate manual page on php.net.
Quick Highlighter supports well over 100 different languages, and when viewing the output you can also grab the associated CSS/HTML. If you plan on using this on a website you could take the time to customize the CSS to your liking, and then later on you can just copy the HTML and use your own custom format that you created.