Source code annotation tool
I'm looking for a tool with which I can annotate source code.
- line numbers can stay intact (for communication with others),
- I can avoid accidentally changing something and
- my annotations stand out compared to the authors comments.
Normally I would print the whole thing out an scribble on it, but the code is too long for that and I need to share it per email. I would be great if one could do some like that including being able to create "links" between so places in the code, possibly even visually with a lines or arrows.
If you would usually print it (if it were shorter), why not print it to a PDF and then use a PDF viewer that supports comments, like Foxit Reader? :)
You can certainly do what you want to with LaTeX and its listings package. But if you are not already a LaTeX user you might think that a hard way to go.
start a github project and post the code there, github includes annotation abilities OOB.
I'd build a glamour browser for it. (If spending half a day building it wouldn't be too much).
 Glamour is a toolkit for building browsers on a model. The model would here consist of the various parts of the file(s) and the comments and attributes you'd like to add. This would allow you to easily navigate through the source and comments, to select only parts with (or without) certain attributes. There is a video and slides. Official page, Source
How about using google wave with syntaxy (http://wave-samples-gallery.appspot.com/about_app?app_id=14008) bot?