[druido]

The icons are found in the Resources folder of the package contents of the respective applications. For OF:

1) close OF;
2) find OF's application icon in the Finder and right-click on it;
3) choose "Show Package Contents".

Some icon files are in Contents/Frameworks/OmniFocusInterface.framework/Resources/ (Context.pdf, Folder.pdf, Project.pdf, …), others are in Contents/Resources/ (e.g., Projects.pdf, etc…). Just replace those files (backup OF first).

The icons I have used are mostly from THL, apart from the Library icon, which is from Things. In those applications, they are stored as png images: I have copied them, converted them into pdf with Preview, renamed them appropriately and put them inside OF's package content.

I did these changes because, for me, the small project and context icons look too similar. Now I can visually distinguish between them much better.
The drawback is that, when you update OF, these changes may get lost.