VPN
Still not very many vpn solutions.
But now http://www.strongswan.org has a pskc11-interface, so the eToken should run with strongswan.
Also openvpn has a pksc11 interface now and runs fine with the eToken.
The sslexplorer which will do the connection via a bowser can of corse also use the eToken 
Desktop
- a tool, that can be used to encrypt single files or directory. i.e. right click on a file in the konqueror and enrypt/decrypt it.
- encrypt a complete filesystem / harddisk
Samba
In fact this missing application is a windows application, but one, that connects windows with the linux world.
A Windows GINA, that is able to logon to a "Samba" domain.