South Mitrovice building 25: "Motel Mitrovica". Having walked all around the centre, having walked past "[the] hotel" several times, thinking it might be the place I was looking for, but deciding it couldn't be and having been given directions several times, eventually I returned to the hotel and it was indeed Motel Mitrovica.
[Corrected on the 14th of January 2007.]
I had thought that it might've been taken down because it was the Serbian spelling, as in Peje, extremists had smashed the sign for the Hotel Metohija (Hotel of the Land of the Monasteries) and in Decan, they had spray-painted out the Serbian spelling on the sign as you enter the town, because they deemed them unacceptable.
Thankfully, however, Anonymous has corrected me that this is:
"Not true, Mitrovice is the name in Albanian but it can also be called Mitrovica. So the spelling is correct. When asked which city are [y]ou from, you can not say I'm from Mitrovicë, so we say I'm from Mitrovica."So, I don't know why it was there, but there's no reason to assume it was related to the other cases that I initially interpreted it in light of.