Hi jdunill,
For the wakeup bit have a look at the free tools at depicus -
http://www.depicus.com/wake-on-lan/wake-on-lan-cmd.aspx.
There is source code, gui and command line tools for WoLing machines. You might need to do some router config if you're waking machines across multiple subnets.
Regarding the backup - ntbackup is a good start, depending on network speed and NAS capacity you might benefit from compressing the backup before copying it over. 7zip is a great free compression tool which I've found to well outperform (both time + compression ratio) some commercial compression software. It is command line scriptable so after the wakeup have a scheduled task backup, compress, then transfer to the NAS.
For the copy itself, have a look at robocopy from Microsoft (bulitin to Vista, or free downloadable in the 2003 resource kit
http://www.microsoft.com/downloads/details.aspx?familyid=9d467a69-57ff-4ae7-96ee-b18c4790cffd&displaylang=en) - it supports multiple attempts, can do restartable copies and has good logging.
Hope that helps get you started!
Simeon