I have a kde3 app installed, as well as kdebase3, it will launch konqueror-3, while I of course want konqueror-4.
#!/bin/sh source /the/kde4_env konqueror $*
chmod u+x ~/bin/konqueror-4
keditfiletype text/html(in your kde3 env) and add konqueror-4. It will create a ~/.kde/share/applnk/.hidden/konqueror-4.desktop which isn't seen by kde4 if you use a different KDEHOME for kde4.
You might have to do the same with a kfmclient-4 script, for applications who call kfmclient directly (e.g. via invokeBrowser).