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To change the icons for Inbox, Projects, Contexts, Due, Flagged, Next Actions, Review, Completed, just use the Perspectives inspector.

You have to hack OF to change some of the remaining icons. Here are step-by-step instructions:
  • Download Stylistica (ICNS for Mac)
  • Create a new folder on the Desktop and drag there the following icons: checkmark.icns, info.icns, like.icns, map_pin.icns, paint_brush.icns, plus.icns, target.icns (these are the ones that I've chosen: you're free to choose different ones). In the following steps you work with this copy of the icons.
  • Duplicate map_pin.icns by selecting it in the Finder and pressing cmd-D.
  • Open info.icns in Preview, choose File > Export..., and save it as a PNG image. Then, delete info.icns.
  • Rename the icons as follows:
    • checkmark.icns => Completed.icns
    • info.png => ShowInspector.png
    • like.icns => MarkProjectsReviewed.icns
    • map_pin.icns => Filter.icns
    • map_pin copy.icns => FilterInactive.icns
    • paint_brush => CompactCompletedItems.icns
    • plus.icns => AddTask.icns
    • target.icns => HoistWindow.icns
  • Select all the icons, press ctrl-c to copy them.
  • Go the /Applications folder and ctrl-click on OmniFocus, then choose Show Package Contents, and open Contents > Resources.
  • Press ctrl-v to paste the icons there.
  • Re-open OF.