I think the niners and maybe the sixers are on the good side of this debate. The best names reflect the area and its lore/identifying/unique characteristic. 49ers isn't really the year, its referening the gold rush/miners, so I think its cool. Sixers is ok too because of the nation's capital (at the time), the war, etc. Likewise, I think the Steelers, NJ Devils, Celtics, Cowboys (yuck), Spurs, Mavericks, Brewers, Magic (hokey as heck, but also reflective of the character of the area), Maple Leafs, Candiens, Canucks, Patriots are all cool names because its not some generic animal aimed at intimidation.
Worst names are Raptors, Jazz, Lakers, Stars, Coyotes (that might pass muster)
I think honorable mention goes to Bears/Cubs, I always liked how the team names were linked.