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If I were building a new MMO today I'd probably use XMPP, BOSH and build the client in Java Script as that would allow it to work without a fat client download and interoperate with XMPP based IM and voice systems (like gchat).
Once Web GL is widely supported this would even allow browser based 3D virtual worlds.
One company that is cool about discussing their implementation is CCP, creators of Eve online.
They have published a number of presentations and articles about Eve's infrastructure, and it is a particularly interesting case because they use Stackless Python for a lot of Eve's implementation.
The game simulations themselves will be built using the same techniques as any networked 3D game, so you can look towards resources for that problem domain to learn more.
Comet or BOSH can be used to allow bi-directional communications over HTTP for web based MMOs and web sockets will soon be a good option there.
For instances (dungeons), usually a new process is launched for each group, which would mean there is a dispatcher service somewhere mananging this (analogous to a threadpool) UDP is the protocol used.
It's fast as it makes no guarantees the packet will be received.
I'd guess the servers will be running on Linux, BSD or Solaris almost 99% of the time.
The server your client talks to will be a server running a daemons or service that sits idle listening for connections.