I'm not sure Trigun has much in the way of a fanbase/fandom anymore... all I know is that I used to be a big part of it and that if the message boards ever start to get moving again, I don't want to be a part of them. This is odd because I have certain AIM friends with who I enjoy other fandoms and talking about life with that I met in the Trigun fanbase. I'm not talking about them when I say I'd rather just shy away from the fandom if it ever starts up again... I made friends, but also enemies and, in general, it just gave me a headache. Shipwars for a very "gen" series, fans' obessive need to diagnose the characers with various psychosies (not that they didn't have them, it's just that having a certain issue myself and seeing the ignorant try to be psychologists....urgh), and most of all, all the "I am right and you are an evil idiot if you disagree with me because my brain is linked to/knows better than the manga-author's!" crap that went on that fandom...
LoZ-fandom has been much, much nicer and more fluid for me. I think I fit it better, perhaps. I love LoZ fandom.
I was watching some Avatar: The Last Airbender today. While I enjoy the show, I never got into the fandom, but having met some of the fanbase-fans in general venues online, I don't think I want to touch that fandom with a ten-foot pole. Ditto for Fullmetal Alchemist. Enjoyed the anime, don't really want to touch the fandom since, like Avatar fans, some of them seem... mean, confrontational - too serious.
Pretty much any fandom/fanbase will have people and factions that will turn you off. The key to enjoying a fandom, I find, is just not to worry about what other people in it think too much - just focus on the thing you like and why *you* like it. Do your own thing with your creative work (if producing and enjoying fanwork is how you primarily define "fandom" - such as with me) and just... don't let the stupidity of people turn you off of something because, frankly, humanity is stupid and you just have to try to ignore most of it in anything you're into.