These fanfics are, IMHO, the best stories featuring Shishiwakamaru. I've put yaoi* and lemon pointers up where necessary. These fics leap about the web like fleas on a griddle, so if a link's broken or you can't find the story on a site, tell me.
Osmalic (the fanficcer formerly known as Ucchan) has written three fics featuring Shishiwakamaru as a main character: "Visit," "I'm Too Sexy," and "Shishiwakamaru's Revenge (I'm Too Sexy 2)." "Visit" is currently missing, which is a pity, since it was the sweetest of the three.
Kuwabara no Miko's sweet "The Eye of the Beholder" is not to be missed. (Thank you for letting me give this fanfic a home, Miko-sama!) [Yaoi]
Sandy Jacobs's stunning "Only Yuu" features Shishiwakamaru in a minor role. Highly amusing. (Shishiwakamaru's role, I mean. Not "Only Yuu." "Only Yuu" is howling-hyena funny.) Shishiwakamaru's main appearances are in Chapters 15 and 21. [Yaoi, lemon, macadamia chocolate chip cookies]
Eek's "Youkai in Black - the Movie" made my brain hurt. Shishiwakamaru as an exterminator, Toguro Otooto as a big-ass bug, Karasu as a... Let's not think about Karasu, OK?
* And someday we'll all be open-minded enough that the mere presence of homosexuality in a story isn't enough to earn it a special warning. Sigh. Better stop before I start ranting. /End Pundit Mode