I don't know if I could choose a favorite even if I tried. So ... list time. These aren't in any specific order save the top of my head.
Naruto [Anime/Manga] (Despite all the bad choices Kishimoto has been making with this, I don't dislike the series. Just the way he's writing it out. After all, not the fault of the characters on what happens to them and such; nah. That's the author's, totally -.-)
One Piece [Manga] (Interesting progress this is making. Can't wait to see how it all goes)
Sword Art Online [Anime] (Seen only up to Season 2. I will try to finish this later)
Rurouni Kenshin [Anime] (I started watching this ... sometime last week and am loving this! I can't believe I never started watching it till now x.x)
Samurai X: Trust & Betrayal [Anime] (One of the shortest series but so very well done. Loved this. Thanks goes to Silverknight for recommending it)
Dragonballz [Anime] (One of the first fandoms I began watching)
Sailor Moon [Anime] (Another first for me)
Pokemon [Anime] (... Yeah, another first. So sue me. I loved the game when I was a child.)
Gundam Wing/Mobile Suit Gundam [Anime] (One of the few sci-fi-esque fandoms that have gotten my attention. Also one of my firsts. Loved this one tons! The movie "Endless Waltz" wasn't too bad either)
Code Geass [Manga] (I've only read "Lelouch of the Rebellion" so far but it was really good)
Fairy Tail [Anime] (Will probably pick up watching once I'm done with "Rurouni Kenshin" but from what I've seen thus far, not bad)
Death Note [Anime/Manga] (Started great, ended horribly. There were definitely some decisions I could have done without, very much so)
Katekyo Hitman Reborn! [Anime/Manga] (Why didn't they show off all of the anime? Meaning, it's incomplete. The entire series is finished in the manga. But more than that, I'm astounded to be one of the few people who knows of this. It's by far one of my favorite fandoms. Yet over the nearly two years I've been on BlueMoon, no one seems to know about KHR! I'm ... astounded o.o)
Usagi Drop [Anime/Manga] (I started with the manga on this one but forgot where I stopped. So I began watching the anime. Honestly, it's better executed in the anime. Highly recommended for anyone who likes slice-of-life types of things. A very cute series! And short)
Onegai Sensei [Anime] (Much like 'Death Note', there were some additions/decisions I could have done without. But all in all? This was a great romance story.)
Claymore [Manga] (Seems like it's trying to get to an ending point soonish. And honestly, I kinda hope for it. Another manga that started out really strong. But now, the plot's getting ... bleh for lack of a better wording)
Yu-gi-oh!, Yu-gi-oh GX, Yu-gi-oh 5Ds, and Yu-gi-oh Arc V [Mainly anime though a bit of manga also] (I refuse to acknowledge Zexal. It was so horribly done and with how dear to my childhood the game was ... no. Just ... no. Arc V is so much better, hands down.)
Kuroshitsuji [Anime/Manga] (Keeping up mainly with the latter more than the anime. So far, so good though)
Romeo x Juliet [Manga] (A nice twist off of the classic book. Highly recommended, especially for those who enjoyed Shakespeare's version)
Waltz in a White Dress [Manga] (One of the best romances ever. The art was really well done in this. I would recommend the anime but there is none. Not that I've seen, anyway. The chapters are long but definitely worth it.)
Doubt [Manga] (Yes, yes, yes, and yes! One of the best horror mangas ever! Loved the concept, was so-so on the ending. But overall? Definitely worth a shot. Another manga that, unfortunately, doesn't have an anime to my knowledge)
Elfen Lied [Manga] (I cried also. Then again, how couldn't you cry? So ... dear lords. Very sad but beautifully done.)
Absolute Boyfriend & Video Girl Ai [Manga] (I place them together because the plot is almost the same .. but with reversed roles/genders for them. Interesting ideas.)
Liar Game [Manga] (Personally, I was amazed to see this one's still ongoing. It had a good stopping point a long while ago. But another thing I'd suggest taking a glance at.)
Hellsing/Hellsing Ultimate [Anime/Manga] (Bloody hell, how'd I forget this? Thanks goes to Halaster for the nice pic which reminded me. But yes .. this is by far one of the best fandoms that includes vampires in it. Holy hell though, they made Seras' background dark as fuck. Definitely nothing I would have ever guessed o.o)
Vampire Hunter D [Book] (So .. sorry if it seems like cheating because it's based off a book. But I'm pretty sure there's an anime too .. but for some reason I can't recall if I have or haven't seen it. Another really good fandom with vampires.)
Vampire Hunter D: Bloodlust [Anime/Movie] (I'm a tad too lazy to add much more so ... pretty much anything that my description for Vampire Hunter D includes for now.)
Petshop of Horrors [Anime] (... Didn't someone like Stephen King or a famous horror author do an actual book on this concept? It sounds familiar. Meh. Aside from that, this was really well done. Definitely one of the better horror series so far.)
Angelic Layer [Anime] (Four words: Make this game real! It would be awesome! While the concept of said game definitely makes the series shine, it isn't the only good thing in it. The characters and overall plot were really well done.)
Chocotto Sister [Anime] (Cute concept. Another really adorable slice-of-life series and the first of it's kind I got into and really watched. It definitely has one of the catchiest ending songs for sure.)
D.N. Angel [Anime] (I'm a bit amazed there aren't many other series that do an angel vs. dark/fallen angel type of thing. Or .... maybe there are and I just haven't found them. Probably the latter ^^;; Just like how "Chocotto Sister" had one of the catchiest songs, it has a memorable one of it's own. It's during the end of Episode 24 .. but personally, I think it should have been the overall ending for the entire thing.)
There are probably more .. but those are the immediate ones I can list. ^^;;