It really depends on the context in some ways and on connotation in other ways.
The bottomline is that a "fanboy" is someone who really likes something... basically a synonym for fan. This isn't bad. I'm sure most posters here can name things that they really like such as games or developers or sports teams. Once upon a time, this would have meant that you were fanboy/fangirl of those things.
However time has passed and, like all things, the nature of the word "fanboy" has changed. Whereas it may have just been somewhat snarky before, many people have come to associate "fanboy" not as "someone who really likes something" but as "someone who likes a product and feels compelled to be hostile to competing products."
The difference is obvious. No longer is it about devotion to a product, it's now has a competitive element of "My XYZ is greater than your ABC." When you put the sports team "us versus them" mentality into anything, rivalries will develop and some will be good-natured while others will be fairly heated. In the world of gaming, rivalries have existed for ages so this is nothing new however people began to use the term "fanboy" more and more which spread the connotation that "fanboys" are rude people that are not your friends.
These days, it's more positive and socially acceptable to say "I'm a Nintendo fan" versus "I'm a Nintendo fanboy" simply because the connotation of "fanboy" has become so negative over the years. It's a somewhat sad development, but hopefully as time passes we will attempt to reclaim this word in a positive light... like porch monkies.