A VPN between windows/linux is a totally achievable hurdle.  I do this 
very thing RIGHT NOW, though I chose to purchase 2 linksys hardware VPN 
routers because of:
1.  Distributing important tasks in a modularized way is beneficial to 
network stablity
2.  The loads already present on my samba server have me scrambling to 
do anything to free resources.

That being said.  You can do a samba connections once that VPN is up.

Performance over the link is good, and is well within usable ranges.  My 
implementation is over 256k DSL lines.  Also, if you have exceptionally 
large data transfers be sure to investigate the perforamnce of the 
different algorithms that your IPSec supports.  Some ARE faster than others.

OR.

You could use ssh tunneling.  I am less familiar with it, but a good way 
to automate is to use ssh-agent.

Kris