I have a lot of favorite fics, and listing them would probably take all day, so here are a few of my top favorites):

*A History of Magic (Puella Magi Modoka Magica)
I've always like history, so this concept of this fic for one of my recent favorite animes got my attention. It looks at the famous women throughout history who were magical girls... and also what that entails.

*The Pony POV series (My Little Pony: Friendship is Magic)
Remember at the beginning of season 2 when Discord basically broke the Mane Six? Well, this story takes a look at the psychological ramifications of such a thing... and BOY is it unpleasant. True, they turn out alright later on, but still, something bad happens to EVERYPONY. And don't get me started on the nightmare fuel... (Note: This one can only be found on DeviantArt, Equestria Daily won't take it for... stupid reasons.)

*The Mouse who Would be King (Kingdom Hearts)
An interesting take on how Mickey Mouse went from a troublesome deckhand to a great king. It's probably noncanon by now, but who cares when the story's so good?

*Fight for the Lost (Mass Effect)
A novelization of the second game, that expands more on the characters, while giving us a great story.

*Death and King's Cross (Harry Potter)
Takes a look at what becomes of certain characters after their deaths, and is sure to give you goosebumps as you read it.

...That reminds me, I should probably update my page on the Fic Recommendation section...

http://www.fanfiction.net/s/6930195/1/MyLittleBronyRealityvs_Fantasy

This would count as a good fic... at least for first 10 chapters. Read it and see what I mean.

I really don't have any other stories you could call 'good', unless you like 2nd person romance fics.

Crossed Paths, Crossed Blades.
Synopsis: A knight of Gondor. A soldier of Harad. An Orc of Mordor. On the fields of Pelennor their lives will cross...as will their swords.
Link: http://www.fanfiction.net/s/4268729/1/bCrossedbbPathsbbCrossedbbBladesb

Battle of the Golden Wood.
Synopsis: The battle for Lorien
Link:<a href="http://www.fanfiction.net/s/1261309/1/TheBattleoftheGoldenWood">http://www.fanfiction.net/s/1261309/1/TheBattleoftheGolden_Wood

The Captain and the King.
Synopsis: AU story - Saruman believes Isildur's Heir is carrying the Ring, so he sends his orcs to capture the Men of the Fellowship. Aragorn and Boromir are taken prisoner at Parth Galen.
Link: http://www.henneth-annun.net/stories/chapter.cfm?stid=83
Other Comments: This goodfic was found in the prestigious Henneth Annun archive and was recommended by Acacia herself on tvtropes. Yes, that Acacia, founder of the PPC itself.

It is an archive for PPCer rec lists.

I keep forgetting to update my list, but it should include OGNA, which I do reread every now and then.

Pokemon Master:
-An AU of the Pokémon anime, Pokemon Master is solely responsible for the Dark!Pokémon fanfictions which have sprung up in its wake. Several years ago, a breach in the dimensional walls allowed Dark Pokémon to return to the world, ravaging and destroy any they come across.

Wings of Council:
-One of my personal favourites, the Wings of Council was one of the first fanfictions I read. The story follows Topaz Soarhire, a young girl who has won the chance to become a Pokémon Trainer. This fanfiction is set in Johto, and includes several original Pokémon.

Retribution:
-Team Rocket has taken over the world, and a secret organisation called Rocket Bane has risen to try to fight them. The story follows a young boy fleeing from Team Rocket and stumbling upon a secret that will change his life.

http://www.thepokemontower.com/authors/acesanchez.shtml
http://www.fanfiction.net/s/831335/1/OnthebWingsbofbCouncilb
http://www.thepokemontower.com/authors/ashjr.shtml

Harry Potter and the Methods of Rationality:
-An AU fanfiction operating under the premise that instead of marrying Vernon (Who wants to name their first child Dudley?), Petunia instead marries a scientist, who passes on his logical outlook on life to Harry. Harry enters Hogwarts with a mind set on giving order to the seemingly chaotic world of magic.

The Brave New World:
-Another AU fanfiction, where Harry feels that Dumbledore has bee manipulating him to achieve his own goals. Harry rebels, and flees to America to continue his education.

Oh God Not Again!:
-Harry accidentally falls through the Veil which takes him to the past, just before he was to start at Hogwarts. One of the best Harry Potter fanfictions I've read, and is incredibly funny.