* Search this blog regarding my previous findings on Jumbo Frames: if you have Gigabit Ethernet & a decent switch, you can use that to speed up your transfers.
* Give this SpeedGuide article a look: there's plenty of tweaks you can try in Vista, 2008, and 7.
* Using a 2003 or newer server/OS? Enable Compound TCP.
* Vista/2008 SP1 & newer systems have some enhancements: there may be inevitable slowness communicating between an older system and these systems due to supporting those changes.
IPv6 is a Red Herring
A LOT of people complain about IPv6 & say its (insert lousy argument). Biggest problem from my own experience seems to be Microsoft's tunneling mechanisms they started implementing back in Windows XP & onward. Rather than disable it, disable the automatic tunneling (its also why some consider it a "security risk"): run the following commands in a command prompt (as Administrator-type user in Vista or newer systems)...
netsh interface ipv6 6to4 set state state=disabled
netsh interface ipv6 isatap set state state=disabled
netsh interface ipv6 set teredo disable
Programs to help with copying
* TeraCopy is something I use regularly at home for making sure stuff copies.
*. If Teracopy doesn't cut it for you (or falls out of your licensing ability), RichCopy is a copy on steroids: multi-threaded copy operations; how to save your files; etc.
*. SyncToy can synchronize one folder to another: you can tell it to copy one side to the other with its changes, or copy both sides & their changes.