I'm using a Debian machine to run bittorrent and other large downloads. I generally copy or move the downloaded files to the Windows machine over Samba. Until upgrading my network to gigabit (with a new gigabit switch and cat6) I hadn't really paid attention to the fact that the speeds were actually quite low -- usually peaking out at 4MB/s. I had previously thought that this was a result of the old 100mbit switch but as it turns out it's not. Both the windows machine and Debian machine have gigabit Ethernet cards, and /are/ running at 1000Mbps full duplex. I have verified the network throughput with iperf to be ~950Mbps both ways.

Here's where it gets weird. Samba, FTP, SFTP, NFS and HTTP transfers are all extremely slow.
Maximums:
Samba - ~4300KB/s (Tested with a simple file copy and Windows 7)
SFTP - ~5000KB/s (Tested with WinSCP and openssh-server)
NFS - 2520KB/s (Tested with the standard NFS client on another Linux box)
HTTP - 3250KB/s (Tested with wget/google-chrome and apache2)

Interestingly they all begin this slowly /except/ for Samba, which with a standard windows drag and drop file copy starts up at around 70MB/s and the speed tapers off at a rate of about 2MB/s/s until it reaces a plateau of around 4MB/s.

Steps I've taken:

Items 1 and 2 on this list: http://www.sysprobs.com/windows-7-network-slow
The smb.conf mods made by the third poster in this thread: http://ubuntuforums.org/showthread.php?t=1908714

The only thing that seemed to help was disabling Remote Differential Compression which I think was the cause for the initial speed burst of 70MB/s.

I've been hours googling this and I'm exhausted so I may have overlooked something... please help...

Are you sure your cables are good? A bad cat5e/6 cable can easily drop the speeds into the single digit MB/s. Are these slow transfers JUST between the two systems, or does either system exhibit these same slow speeds when accessing other network resources?

I've replaced all cables concerned twice, and as I mentioned above, iperf tested a perfectly good speed between all computers involved. It's a samba thing. Or (more likely) a Windows issue. If I try a similar file transfer between the debian server and an ubuntu laptop, over the gigabit ethernet, the speed hovers around 29MB/s, which is definitely not a gigabit speed either, but it's a lot better than 4MB/s.