We have been building/installing VPON systems (Linux DOM) for the last 3 - 4 years. The ease of DOM's have made us stay away from Windows systems. That said some pros and cons on linux:
Pros:
1. OS not HDD dependent
2. Don't have to pay for the OS
3. Fast COLD BOOT
4. User friendly - specially using the IR Controller
5. Truly Plug-N-Play
6. Remote Firmware Updates
7. GUI customization using local/remote FTP
8. Minimum/No installer/user interaction - post installation - no windows updates, AV, etc
9. IDIOT Proof and dedicated - hard to mess up the DVR Core even if the user tries hard
Cons:
1. Need specific hardware - specially VGA and Audio Cards
2. Web Servers are not that Windows friendly - specially with Vista (ActiveX signing issues)
3. Video quality not up to par with windows contenders (similar priced)
4. Need a Laptop or linux/windows boot (rescue) CD to work with the DVR HDD's
5. No multitasking - PC becomes a dedicated DVR -
These are some of the pros and cons off the top of my head and based on the VPON DOM Model.