Ron said:
Use linux as your primay OS and run windows in vmware.
Why would you install VMWare on a server?
Anyway, iptables in Linux can be better compared to Windows Firewall than "DDOS" protection. Sure, it's a very useful tool- it may even be an essential tool for some things- but it's silly to call a (software) firewall sufficient protection for a Distributed Denial of Service attack.
Think of this diagram:
Let's assume iptables is on the computers in the above diagram from Cisco. The bandwidth causing the "Denial of Service" would need to be more than your computer's capacity, and less than the capacity of your ISP and also less than the capacity of your router or any other interference.
It's very unlikely the affected service is actually the server containing iptables- and even if it is- there is still a point where more bandwidth could overwhelm the system; Any software on either computer is not a solution for arbitrary numbers.
A good solution would deny your services to the attackers at the earliest possible point- which usually isn't an option. Like jMerliN said, there are services (which may be expensive), but manage to mitigate DDOS attacks.
The battle between "software" and "hardware" firewalls is a joke. Every piece of computer hardware has software to drive it. Obviously you need both hardware and software to route some incoming requests while rejecting malicious ones. It's where you put this device that matters more than the hardware/software you use- such as iptables or some other firewall.