Maybe it's time for a Windows application plus a Maemo 5 app that allow downloading the .install-file (and whatever it points to) on the desktop PC, transfer it via USB to the N900 and trigger the install procedure there.

Probably a Windows version would do. I simply assume most GNU/Linux users wouldn't need it.

Simply running dpkg -i <package> from the command line on an N900 that's offline can be tiresome if the package pulls in a lot of dependencies.