There absolutely are different types of ports and different quality. Whether it's done by Nintendo or a third party is not necessarily the most important thing though. I think it does suggest something as far as quality though. If it's Nintendo doing it, and it's a popular game, then you might have a quality port. If it's a 3rd party...ehh...

I think ports are a good thing for system owners if the company actually takes the time to do a good port. Sometimes they don't, unfortunately. People don't want to own every system, and they shouldn't have to. Some people have even been known to have the same game on multiple systems, just for the ease of playing a game they really like without having to setup a different system.