There's a fantastic Marvel fanfic called Polarity that has the B-list villain the Shocker as its protagonist. It's well-written, everyone is in character, and - best of all - no character bashing!...Except for Electro, but we can chalk that up to...well, just read it.

https://www.fanfiction.net/s/5124106/1/Polarity

There's also a very good novelization of Breathe of Fire II that I can't say enough good things about. It's funny, at times horrifying, and gives a silent protagonist a believable, well-rounded personality.
https://www.fanfiction.net/s/6615342/1/Breath-Of-Fire-II-War-Of-The-Demons

So I'll post the link to my rec centre here, since they all come with descriptions and whatnot. http://ppc.wikia.com/wiki/PPCRecCenter/EileenAlphabet%27s_List
My favourites tend to be crack/humour (especially Mare Sue parodies like Ensign Sue Must Die) but there are a couple of serious among them.

And then I would like to add Bed of Thorns which is a Once Upon a Time fic. http://archiveofourown.org/works/377718/ NSFW. Contains naughty bits. Tasteful naughty bits, but naughty nonetheless. It's an AU that focuses on Belle and Rumpelstiltskin and this was the fic that made me realize that I actually do like romance (and erotica), when it is done properly, (by someone who actually knows how the female body work).
It is a huge work, focusing on character- and relationship development and even if you don't watch OUaT you should consider reading it anyway, for it is a shining example of goodfic. The level of research and attention to detail is mindbogglingly.

Here are some of my favorites, both old and new! (you can see these and some others on my ff.net profile)

https://www.fanfiction.net/s/10366090/1/The-Free-Fighter-and-the-Evil-Within Haruka has magic water powers and it's awesome.

https://www.fanfiction.net/s/3964606/1/Alexandra-Quick-and-the-Thorn-Circle Harry Potter fic set in wizarding America. Very very interesting, and part of a whole series!

http://s7.zetaboards.com/Nuzlocke_Forum/topic/8771921/1/ Post-apocalyptic FireRed storylocke. Funny, touching, and appropriately creepy.

http://www.fimfiction.net/story/34694/a-pony-out-of-place I remember liking this when I read it. A Ponyta from Alamos Town falls into Equestria because of the Dialga/Palkia battle. Cute and believable, especially Twilight's reaction to him using Sunny Day.

http://www.fimfiction.net/story/11343/another-day-for-the-whooves This fic has it all; cute Whooves family slice-of-life, time travel, alien-related insanity, and of course, muffins!

http://www.fimfiction.net/story/1990/waking-nightmares BLU team enters Equestria. Everything snowballs from there, but in a very good way.

www.fanfiction.net/s/10399457/1/As-We-Go-Along Series of short fics involving Jamie and the Second Doctor. Very, very fun to read.

www.fanfiction.net/s/4469720/1/ Like making fun of slash pairings? Read this!

http://archiveofourown.org/works/981746 OH MY GODS THE LEVELS OF SHIP TEASING AAAAAAAAA!

http://archiveofourown.org/works/1062757/chapters/2131218 Night Vale/His Dark Materials crossover AU. It's beautiful and funny and Witch!Old Woman Josie is best Old Woman Josie.

The Particular Problem of Postern Prison

This is a Sherlock Holmes (not Sherlock) fic that features a younger Holmes that has not yet met Watson. It is not the only fic the author has written (she has 31 on FFnet). All of her stuff is amazing, but this is my favorite. I would pay Real Life money to have this as a real printed and bound book.


On the Road to Come What May

This is a Stargate Atlantis fic. It features an entire cast of OC's that carry the POV, and the story is really how the SGA cast affect the lives of that OC cast. But it is also about the SGA cast in a terribly difficult situation and they are all wonderfully in-character.

The Names Upon the Harp

This is a LotR fic. Try not to read the summary, it is a spoiler. If you can't help but read it, the fic is still powerful. Seriously, I cried. It is sort of in-between the movie verse and the book verse, and if I say anymore, I'll spoil it.

Body Parts

This fic is by Roveare11, who is now my Haven beta. She has a lot of fics written and I love all of them. I am including this particular one, because I have been reading fanfic since 2003 and this is what finally prompted me to start writing fanfic. You don't need to know Haven canon to read this fic. Everything you need to know is pretty obvious from the fic, I think. One of her best qualities in Haven fanfic is that she always gets the dialogue so perfectly in-character.

The Very Inappropriate Misuse of Stark Technologies

This fic kicks off a whole series of hilarious fics that are logs of emails, texts, twitters--that sort of thing. Anyway, good to read if feel like laughing.

I have more! But I've got to get to work now.

Here's a good dimensional snatching one in the Legacy of Kain series that doesn't require canon knowledge to understand. https://www.fanfiction.net/s/1329325/1/Urban-Nosgothic

She also wrote her fursona into LOTR, but I never got around to reading it. https://www.fanfiction.net/s/1155355/1/Necklace

Then there's this one, which is excellent. https://www.fanfiction.net/s/1908163/1/Intruder-on-the-Set

This is another Legacy of Kain snatching by a different person. https://www.fanfiction.net/s/1408150/1/The-Pygmalion-Syndrome