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There's a sticky with a list. Also, I know a couple really good ones from back in the old days....
...or at least I remember them being really good, heh.
Not sure if I ever got to posting em...

So sad... they were all chased away by the crazy Marry Sues and fan girls. gonk

There's a REALLY good one for MalikXMarik and RyouXBakura on Fanfic.net called Egyptian Sensations and it's by someone called mewchoochoo
They are VERY good and there's good description, humor... and it's just that awsome. You should check that one out if either of those pairings meet you likeing... however, the main focus of the story is RyouXBakura.
It's also fairly short, but it's more than just one chapter.

Here y'go!
I'm a fanfic-aholic so here's my faves!

Puppyshipping:
Behind Blue Eyes (******)
http://www.fanfiction.net/s/2563712/1/
and it's sister story:
http://www.fanfiction.net/s/2984194/1/
Fair Play (** funny )
http://www.fanfiction.net/s/2910616/1/
Blind Love (**)
http://www.fanfiction.net/s/1599595/1/
Family of Dragons (***)
http://www.fanfiction.net/s/1873209/1/
Forget Me Not
http://www.fanfiction.net/s/2550116/1/

Puppyshipping:
A Requiem for Innocence (*******)
http://www.fanfiction.net/s/2497412/1/
It's a Wonderful World (*******)
http://www.fanfiction.net/s/2427964/1/
Sennen Rage (*******)
http://www.fanfiction.net/s/2643237/1/
And its sequel:
http://www.fanfiction.net/s/3483375/1/
Artisan's Craft (***)
http://www.fanfiction.net/s/2788310/1/

Here's my summaries, well, kinda.. ^^
BBE is proabably my absolute favorite Puppyshipping EVER! A must-read! And it's sister story is just as good!
FairPlay is HILARIOUS!! just read the summary and you'll want to read it. But it's also really good!
Blind Love is so sweet! Lots of WAFF along with a bunch of angst (Jou is going blind not his sister. Interesting much??)
Family of Dragons- Absolutely GEORGEOUS!! Too good for words! Its worth it even if the authoresses only post once a year (I'm serious ) Also, their photobucket is incredible! Packed w/ Puppyshipping photos! The account is KaibaisWHATp and the password is puppy ^^
Forget me Not- also very sweet, and angsty at the end!

ARforI is absolutely incredible!! It was proabably one of my first fanfics ever! A must-read.
It's a Wonderful World is un-be-lieveable! The authoress is just incredible, you have to read her stuff!
Sennen Rage and it's sequel story Strike Records is just so good, very angsty. Lots of problems and dark stuff, but with just enough fluff to keep any fangirl happy ^^
And finally Artisan's Craft is just great. It's a completely new plot from the show which is nice to see.

Anyway! Those are my favs and I have more where they came from at my profile (www.fanfiction.net/~pharaohess1). Just skip by my only story, it was a gift and it wasn't even YGO sweatdrop PM if you want more ^^ :is finding more as she types but doesn't feel like adding them: