To add another dimension to the topic, what is it that makes a good town for you? Is it the layout/ease of navigation? The music? The cool townies? The architecture?
Obviously, it's a combination of things. But I'd have to say that the best towns have their own unique feel to them. Not just village after village of Germanic/Scandanavian-stye houses (Final Fantasy 1-5, Tales of, etc...). But on the fipside, the best towns don't just take one exact style and copy it over and over again, each building has its own individuality befitting of its purpose. So, instead of an inn just being a residential house with a sign over the door, it might have a more commercial look to it, might have spiffy gables to attract custormers, etc. Thirdly, and possibly the most important, a combination of navigational clarity + speed of navigation (including load times) is very important. YOu can have the best designed, most immersive town in video-game history, but people will simply be a burden if the camera angle makes it impossible to navigate, if its slow to move around, and you're faced with 10seconds of load time ever 2 screens.
So here's the list:
1. Uniquely cohesive feel for every town (denoting differences in culture)
2. Individualistic styles to buildings befitting their function and to add variety
3. Well laid out Navigation system, speed, and low load times
Most games are able to gt #1 fairly well these days. Ever since the yawning moments of the SNES (FF6 on), designers have had lots of fun creating a sense of "culture" for each town. #2 is a little bit less common. Actually, #2 was done a little better during the Pre-rendered days of the PS1, when static camera angles mixed with individualistically photoshopped 3D "paintings" allowed every building to have its own unique flair. The fully 3D era has been a little hard on #2, because, in a way, we're back to "chipset" design philosophy, just in 3D space. #3 has always been a problem. Some of the finest towns also provide the worst navigation. "interesting architecture" sometimes makes for confusing navigation.
Many people point to Rabanastre from FFXII as a great city. However, while I think it absolutely excells at point #1, creating a very unique and realistic cultural atmosphere, a lot of its architecture becomes too repetitive. Additionally, somehow about the camera positioning made me feel like I was never looking out across the city, I was always looking slightly down, so I never got to view the tops of buildings or the sky to get my bearings. While I would say that Rabanastre was a wonderful creatioin, I never really found myself "enjoying" it.
I don't think any RPG has gotten it close to 100% correct yet. Skies of Arcadia and Grandia II are probably the most enjoyable so far, with maybe FF9 coming in third.