Now days both operating systems are very stable. Reboots are to a minimum whenever you add or upgrade, but Windows still requires more reboots in that respect. Both provide very comprehensive security and stability update notification services.
The largest difference is migration. To move from one Windows server to another, you must build the new server and then create each instance or object and then import the data. With most Linux services, after building the new box you just copy a few config files and the data.
If you still have not decided which operating system to go with, first inspect your checkbook and then go on to read the Windows 2000 Server installation guide and then the Linux Installation Guide. Hopefully this will be enough mental punishment to force you to a decision.