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Otaku is derived from an honorific Japanese term for another's house or family (お宅,　御宅 otaku) that is also used as an honorific second-person pronoun (roughly equivalent to usted in Spanish). In modern terms, it means roughly that the person all their time in a house(or other place), doing a particular thing(watching anime for extended periods of time would equate the person to being an anime otaku, while practicing your tennis techniques for vast amounts of time would make you a Tennis Otaku, etc.), and typically means that person has little to no social life. Consequently, this terms carries a great deal of negative weight in it's native country. There are even particular terms for certain groups of the super obsessed(Fujoshi (腐女子, "Rotten Girl"?) is a pejorative Japanese term for female fans of manga and novels that feature romantic relationships between men. It is also a homophonous pun on fujoshi (婦女子, fujoshi?), a term for respectable women. The name originated with members of the demographic, who self-deprecatingly refer to their way of thinking, which perceives homosexual relationships between male characters in stories that do not include homosexual themes, as being "rotten".)

Despite this, there have been attempts to take away the impact these words have and try to make them something positive(something international fans have been trying for year and years). In English, it is used to refer specifically to a fan of anime and/or manga, though it can sometimes refer to any kind of "geek". It also is used to refer to people who appear to be obsessed with Japan and its culture, and also has it's own specific pejoratives(Japanophile, Wapanese, etc).

What I want to know, is that do words and labels like these have an impact on how society perceives fans of the form? Should they even matter anywhere? What of your own tales of fandom?

Remember, I MODERATE here. And generally, Otaku means geek, but in the sense of weight the Japanese feels it carries, it's closer to shut in nerd or a super geek. And whoever said otaku isn't Japanese should slap themselves(especially if they can't even recognize an honorific form of one of their their own words)

When I learnt that word in class... my teacher didn't say it was something negative... just that it meant "fan" ( anykind of..) or refering to "home", "your house"... maybe "somene else's house" too (not sure about that)

Yes, I get annoyed with alot of people who think they're cool because they call themselves otaku, but they don't really know what they're calling themselves (I think we shouldn't change the usage, it makes us look ignorant).