2. The Year of Living Quietly (http://spn-summergen.livejournal.com/17411.html) - How it starts is Dean is fifteen and Sammy is eleven, and Sammy stops talking.

4. Life Used to be So Hard (http://roque-clasique.livejournal.com/37000.html#cutid1) and the prequel Preservation (http://roque-clasique.livejournal.com/56447.html) featurea traditional werewolf!Sam, but they are excellent and you might like them.

As far as shapeshifting into animals, I only know of a couple 'cursed into animals' fic: Puppy Dog Tails (http://rahmi.livejournal.com/133527.html), where Sam and Dean are turned into their spirit animals temporarily. Twice. Also Stray Cat Blues (http://teashopmuses.livejournal.com/45629.html), where Sam and Dean are turned into cats.

5. These may or may not be what you're looking for:
Most Likely To... (http://monicawoe.livejournal.com/46527.html) - In which Sam saves some college buddies from a dragon monster and they are less than appreciative.
Never Summer (http://ignipes.livejournal.com/82858.html) - A call from one of Sam's college friends brings the boys to a remote Colorado hotel in the midst of a blizzard to investigate a death and a haunting.
Sam's Best Friends He Doesn't Know About (http://clex-monkie89.livejournal.com/664576.html) - Five people who helped Sam in Stanford.
And They Cry to See Your Face (http://honeylocusttree.livejournal.com/54465.html) - Some of Sam's college buddies get rescued by him and Dean, but he's not the man they knew anymore.