I'm currently using SMB for my Windows hosts, and I'm only backing up C:/Users/* on most systems. I also backup some MSSQL database backup directories on one host, and a Quickbooks folder share on another host. I have found over the years trying to backup all of the Windows file-system just isn't worth it for my purposes.
And for anyone who may be interested, I'm running BackupPC 4.0 as a KVM virtual guest on a Core i5, with 2 of the 4 CPU's, and 8GB of the 16GB of RAM. 4 SATA Disk RAID 10 running the virtual host and guests. Has been working quite well and been plenty fast for my needs.