The /home/QtPalmtop/etc/mime.types file contains the list of the file types recognized by the Zaurus. The /home/QtPalmtop/etc/slmime.types file contains the directories where the Zaurus will save a specific file type. Changing those files (and restarting Qtopia) can help to achieve what you're looking for...
In the .desktop file associated with your application, you'll find the mime type with which the application is associated.
Say, for instance, that you want to open .pdb plucker files with Opie Reader.
Its .desktop is /home/QtPalmtop/apps/Applications/uqtreader.desktop (or something like this, depending how/where you installed it).
In this file we find the line:
MimeType=etext/*
so if we modify the /home/QtPalmtop/etc/mime.types file to add one line like this:
etext/plucker pdb
and then reboot the zaurus, the .pdb plucker files are shown with the appropriate (Opie Reader) icon, and tapping on such files automatically launches Opie Reader with that document opened...
Hope this helps!
PS: Maybe there's a quicker or more efficient/elegant way... The same question has been somewhat bothering me for a while, so when I saw your post I decided to have a quick look at this, and that's what I could gather so far... Any hint / correction / addition welcomed!