OK, someone totally needs to write VM/mini-Jack. Well, not in a shippy way, but as an excuse for a snark-off to end all snark-offs. Having him transfer to Neptune High is pretty minor as crack-addled AU devices go.
Fay, I'd say to stay away from VM fic until you're done with the season, because a lot of fic spoil for the identity of the rapist & murderer, and if at all possible, I'd recommend watching the whole season unspoiled.
I haven't seen that many Logan/Weevil fic despite the rampant slashiness. Come to think of it, I can only count a handful of stories I found memorable, full-stop. There are fic (largely het), but most of them are so-so in quality, and the best ones are set post-finale. (I think all the best slash writers have gone to SGA fandom.)
You're about half-way through the season, right? We have a few stories at BSO, but most of them are spoilery for the finale. Hmmm. Let me see if I can round up some non-spoilery recs.
Silvia Kundera's "This Is Not Ironic". [link] Weevil fic, mostly backstory spec and not spoilery.
Mosca's "Nobody Wants to Uncover". [link] Weevil/Logan set around "The Girl Next Door" (the deeply slashy detention episode.)
Another good post TGND fic: [link]
Hawt and snarktastic AU version of "An Echolls Family Christmas" (the poker episode), "Snark Never Goes Out of Fashion" (Veronica/Logan) [link] One of my favorites.
Fucked-up Veronica/Logan/Duncan (not spoilery post ep. 1x08), "History" [link]
Short but evocative Logan-centric ficlet, "The Scent of Blood Orange" [link]
I like Fox's "If It Makes You Happy" a lot , which is a Veronica/Logan circa 1x10 and is messed up and ouchy in the best possible way: [link]
Hawt Weevil/Logan/Veronica smut, "Sweeten the Pot" (set during the poker episode): [link]
Totally adorable wee fic about Logan and Duncan meeting for the first time in the kindergarten: [link]
"Family Ritual", which is about Aaron and Logan during that scene in "Return of the Kane". It's pretty fucked-up, and altogether believable. [link]
OK, that's as many I can dig up in early episodes-centric fic. As a rule, the LJ community vm_fic (http://www.livejournal.com/userinfo.bml?user=vm_fic) is a good place to go; they catch most stuff that are decently written and characterized, and they ladies who run the community helpfully label the fic by the episode they spoil, which is a huge help if you're not done with the season.