Permanently indicate to Market an application should refuse upgrades?
Titanium Backup Pro can do what you want. (Yes, you must buy PRO. The feature is disabled in non-pro).

Once you have the app, do this:


Open Titanium Backup Pro
Open tab Backup/Restore
Scroll to the app that you want to unlink from Market
Long-press on the selected app
Click Detach from Market


I can't get it to work on my phone, but maybe it'll work for you.