I currently run a company (on the IT side) with 100+ servers...a healthy mix of both Windows and Linux. To write-up the benefits I see of Linux over Windows would take a fairly long blog post...perhaps I'll do that soon. However, I will say that the last time I had a Linux hardware problem which wasn't related to a display driver issue (and in other words, not on the server) was in 2006. Our Linux servers are reliable, easily configured (admittedly....we know what we're doing) and have very high up times. Contrast that with our Windows servers which at this point we've had to resort to weekly reboot Windows to keep them performing.

Personally, I also find it much easier to find help online with Linux when things do go wrong...and that Microsoft (wisely) makes the whole experience very painful unless you're willing to pony up for their more expensive "tiers" of software. As an example, even though DFS-R is included in Windows Server, try managing a real, live deployment given what you're provided with just Server. Unless you purchase SCOM, your will fail.