Always when I deal with big projects, the first thing I do is organize a strict file structure. Not just web2py, I do similar things with photoshop layers, files on my computer, etc. It just makes life that much easier.
For now, I would just reorganize your file names a bit... ie.: /controllers/result_grid_service.py /controllers/front_service.py /controllers/import_wizard_service.py /controllers/export_wizard_service.py to /controllers/service_grid_result.py /controllers/service_front.py /controllers/service_wizard_import.py /controllers/service_wizard_export.py etc. So prepend "service" or "services" as it would be a directory. Use "...wizard_import.." and "wizard_export" instead of "...export_wizard..", do "grid_result" instead of "result_grid", etc.. If you do it this way, everything stays alphabetical, "wizard" controllers will be listed together with other "wizard" controllers, "grid" with other "grid"s, etc. If it's the visual presentation that is the main issue here, than this will give you a very similar result as subdirectories would. Except that you'll still see all the files at once, which I don't think is such a big deal. Plain, not rewritten URL-s will also be very similar as they would be if you had directories. Problem solved?