Most likely Bleack. As a soul reaper, and one with a really awesome Zanpakuto. It would be a gunblade that shoots, despite how unreasonable that is.

I would to be in inuyasha, naruto, sailor moon, fairy tail, blue seed,medabots oh yeah theres tenchi muyo too so many....

I will choose pokemon.

That's hard. Not to say I haven't thought of it though. One Piece would definitely be one. I can just imagine sailing with them... Would be fantastic. Also, Meeting the crew would be also really freaking awesome. I would pick Fullmetal Alchemist, but there's mainly two reasons I'm not. In the Original, SPOILER ALERT! SPOILER ALERT! He winds up staying on earth in the Movie, so essentially, I already live their. Not to say I wouldn't want to Live on Ametris either. It's basically earth, but with Alchemy. Again, SPOILER ALERT! Edward changes Ametris so that Alchemy can't function there. Oh and one other reason, the Time Lines are about a hundred years around ago.

One anime that I'd want to be in, would be Persona 4. Yeah, this WAS originally a game, but they made an Anime out of it. So... that counts? Right? Honestly, I'd love to hang out with the cast from the game. Would be a hilariously, fun time.

With that being said, One Piece is still probably my highest choice.

I would immediately want to be in HoTD (High School of the Dead)... why, well that's really really simple...

1- I get to kill zombies (HELL YEAH! 'Murica!)
2- That way I can fix the anime by killing off Takashi who is a selfish lowlife and Hisagi & Rei who are both snobby b****es.

It really isn't a fair choice, but Dragonball/Dragonball Z. Think of it, ANYTHING YOU COULD POSSIBLY WANT, just by collecting the dragonballs and wishing for it. You could take them, wish to move to a different dimension(AKA different anime) and have the wish make the dragonballs follow you. Endless possibilities.

For me, it would be Code Lyoko. The school the characters attend(Kadic Academy) is actually based on a school in France(Lakanal College) and the Factory that contains the Supercomputer(and consequently the virtual world they do battle on), was based off an actual abandoned Renault Factory(which has since been demolished). The show had been in reruns or off the airwaves for 5+ years until this past January when Code Lyoko Evolution premiered. Evolution is essentially Code Lyoko's 5th Season, but being its now in a Live Action/3D CGI format I am not sure you can call it an anime anymore. My powers on Lyoko would be support based and my unique ability would be to heal/restore life points in the heat of battle. This of course would make me the primary target so I have a shield to defend myself.

Hahaha if I could be in any amine it would be One Piece. I be an hand to hand combat master, and I would have eaten an devil that lets see here........ gives me the power of nature, plus shadows. The Nature nature fruit and the Night night fruit.

I would pick Clannad, being Tomoya, I know his life turns to complete crap but I feel that I can really relate to him.

I would probably have to choose between Bleach and Pokémon.
Bleach because you can fight with Zanpakutos, use Kido, kill friggin Hollows and all that amazing stuff.
Pokemon because you get to have a partner for like all life, go on an adventurous journey and probably not having the chance of dying as fast as in Bleach :p

Now that I think of it, being in Higurashi or Umineko wouldn't hurt either. Being surrounded by crazy, sadistic killers would be nice.

DN : Okay, before you go on telling people that the main character is everything, that isn't entirely true. If you look in the video games section, you may find a thread asking what video game universe to be in. If you look on that thread, you could find some people want to be NPCs, such as Toad in the Mario series, or enemies, such as a Stalfos in The Legend of Zelda series. So no, not everyone wants to be a hero.

Edit: Forgot to include my own thoughts. I have mixed thoughts, actually:
Pokémon: If I was still male, I'd want to create a protagonist team to counter one of the antagonist teams (eg. I could make Team Gravity for Team Rocket, Team Polarity or Team Clear for Teams Aqua and Magma, Team Void for Team Galactic, and Team Reactor for Team Plasma). Here's some info for the possible teams:
-Gravity: Team Rocket say they blast off again, Team Gravity would say they land safely and properly. While Team Rocket steals Pokémon, Team Gravity would donate Pokémon to professors and upcoming trainers.
-Polarity: They would counter Aqua by rescuing Kyogre with the intent of freezing the foiled plans through Sheer Cold, and they would counter Magma by pulling the landmasses around through the amplification of the magnetic poles of the planet which attract the ores deep underground in the landmasses. Team Polarity would gather Registeel, Regirock, Nosepass and Probopass for this.
-Clear: They would work hard to find Rayquaza to stop both of Hoenn's antagonist teams.
-Void: They can use the opposing Pokémon of the paired games, or in the case of Platinum and maybe the anime, encourage Giratina to take further action. In the end, I would tell Cyrus that it would be impossible to preserve everyone to be carried from one universe to the next.
-Reactor: Plasma wants to pull people and Pokémon apart for Ghetsis' gain. In the first incarnation, Reactor would spread the message of the player and Alder, that Pokémon's feelings grow alongside the trainer, that is a bond, a strong connection between trainers and Pokémon. In the second incarnation, Reactor would welcome the second player character into the team and work together to get all the Pokémon back and save Kyurem.
...but I digress. If I could choose to be female, I would either do the same as above, or hang around a good male trainer, or I'd be a beautiful shiny Gardevoir or an adorable Eevee or Vulpix.
Dragon Ball Z: I'd either be a human that trains harder than Krillin, a saiyan that trains harder than Vegeta, or a Namekian that meditates with more focus than Piccolo.
Lucky Star: This is the first time I ever considered Lucky Star. I'd either be a boy that works hard to hunt down the girls, or a girl that obsesses over Kagami's tsunderity.

I consider games with anime art style or games that generally use anime gags can qualify in the anime genre. So...
Hyperdimension Neptunia: Either a male NPC that tries to hunt the girls down, or a female DLC that likes the DLC character Red.
Osu! Tatakae! Ouendan: Probably some random person that walks by and feigns interest in the events taking place in each level.
Atelier: Probably a female NPC that just behaves in a way that increases the rating of the games.
Project Diva / Vocaloid: A new singer with mostly hip-hop, metal and country songs.

Oh wow nice post uh hum wow it would be hard to choose over dragonballz or naruto shippuden eh.. I would choose naruto shippuden.

I would be in DBZ as a person called Fred 

I would want to be in Bleach, because I enjoy Sword Fighting and in Bleach I could max out my katana duels

Bondage fairies.

Well, at first I was thinking Pokémon, but then I realized that I wouldn't really be doing any fighting, so I think I'll choose Bleach, or maybe a romance like Marmalade Boy.