Err.... a linux machine can stay up for years assuming a ups - 2 months is not a long uptime. I think that eqemu stability is a function of the number of users. My server, which only has 6 users, stays up for months at a time. I'd suggest that you run whichever OS you know best - for myself, managing a NT based server is challenging, whereas a linux based server is simple. Others will see it the other way around.
I believe that remote management is simpler under linux, but that's just because of its heritage, and is also merely an opinion. If you know how to lock down NT, and are happy with point-and-click, or know how to use its arcane command-line interface, then use that. If you want to run eqemu in a chroot jail, manage it through ssh, or push it across your network in a strange way (i.e. across an IP-IP tunnel) you'll find linux easier.
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