Here are two short applescripts that can be used to change the application that is used to handle a certain protocol in Netscape Navigator¬: one to set Eudora as the application to handle all "mailto:" URLs, and one to set Archie as the application to handle "ftp:" URLs.
These AppleScrips can be modified if you want other preferences, the sttructure of the script is:
tell application "Netscape Navigator¬ 2.02"
register protocol "Xxxx" for protocol "Yyyy:"
end tell
in which "Xxxx" is the creator type of the application that must handle the protocol ("CSOm" for Eudora, "Arch" for Anarchie), and "Yyyy:" is the protcol part of the URL ("ftp:" for file transfer, "mailto:" for e-mail).
The settings can also be changed by ResEditing the Netscape Preferences file, but I am not certain which changes must be made (it looks like the STR# 2003 resource is involved).