I've found that the Linux based EQEMU server tends to have more bugs due to slight differences between the Windows libraries and the Unix libraries.
My suggestion is the following:
1) If you are comfortable with c++ and you want to run an arguably faster, tighter server with a few more bugs, and you wish to track them down, fix, and contribute then go with Linux.
2) If you want to run a server for entertainment purposes and prefer to stay out of the code, then Windows is your choice. The small/large/whatever performance gain by using Linux isn't worth the hassle of zone server crashes and login bugs (not that those don't happen on windows).
Regards,
krich
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