For #1, Sam's reaction to John's death:

Broken Souls And Tired Regrets (http://halfshellvenus.livejournal.com/334880.html) by halfshellvenus -- (gen) -- Summary (post-2x01, "In My Time Of Dying"): Dad's gone, but for Sam that shadow still remains…


For #2, shapeshifters:

The False Comforts AU (http://chaikhana.net/spn/fc_index.html) by Maygra


For #4, AU fics:

the Turn of the Wheel Series (http://gekizetsu.net/sn/wheelmain.html) by eighth_horizon -- (eventual Sam/Dean) -- the guys keep running into (or rather, getting bitchslapped by) elementals.

The Salvation Future 'Verse (http://assignations.org/spn/fa_index.html) by eighth_horizon and Maygra -- (Sam/Sarah. Dean/OFC, some Sam/Dean) -- I know it looks huge, and it is, but it's an amazingly satisfying world to enter.

Secure the Blessing (http://rahmi.livejournal.com/97723.html), the sequel Up Ahead (the roads were closed) (http://rahmi.livejournal.com/203756.html), and the timestamps (http://rahmi.livejournal.com/230508.html) by rahmi -- (gen) -- AU. When Dean is killed in a fight with demons, Sam in grief and desperation wishes that John, Mary, and Dean live. That they know what "normal" is; that John never has to teach Dean how to be a soldier.... and that Sam is kept away from them because supernatural evil is always attracted to him and he doesn't want it to touch them any more. Of course wishes never go the way they should, and Dean wakes up in a 4 year-old body with most of his memories intact and starts demanding that they produce his Sammy immediately.

Dragon Spell (http://virtualpersonal.livejournal.com/206751.html) by virtualperson and brimstonegold -- (Sam/Dean) -- AU. Crossover with Dragonriders of Pern. Sam finds a scroll in his dad's storage locker that transports him into a world where dragonriders must protect their world from a continuous threat of threafall. Dean finds a way to follow him and finds Sam has no memories of his previous life. There is some non-con due to another character who is in a position of power over Sam. This link is to the master post.

This is the Sun Gone Down (http://fourfreedoms.livejournal.com/120803.html) and the timestamp This Space Will Never Get Tired of You (http://fourfreedoms.livejournal.com/138777.html) by fourfreedoms -- (Sam/Dean) -- The first story is a fascinating examination of what things would have been like if Sam had Dissociative Identity Disorder. Told from Dean's POV. The timestamp is Sam and Dean's first time together after Sam's integration, with special bonus powers!Sam.

The Cartography 'Verse (http://ignipes.livejournal.com/tag/cartography) by ignipes -- (gen) -- Sam is living alone, and it's been 2 years since Dean died... until Lenore appears. With Dean. Except Dean has no memory of who he is, or who Sam is.

Five Districts, Five Drugs (http://rei-c.livejournal.com/tag/5d5d) by rei_c -- (Sam/Dean) -- link to the master page. This is an amazing 'verse that I'm including just in case you haven't read it yet.