Hey! I've got some recs that I hope you'll like. I only read gen so I can only rec the last few points on your list.
Fics where Sam is hurt and John in protective: I'd recommend looking at skagtrendy on ffn (https://www.fanfiction.net/u/1397836/skag-trendy) and Menthol Pixie (ffn (https://www.fanfiction.net/u/18504/Menthol-Pixie) and LJ (http://mentholpixie.livejournal.com/)) who both write a lot of hurt!Sam and John in a positive light, if you have a look through their fics I'm sure you'll find something you like. Kokoda2007 (https://www.fanfiction.net/u/1303844/kokoda2007) has a lot of hurt!sam with some guilty John and Dean Also: Wired (https://www.fanfiction.net/s/4264997/1/Wired) by Faye Dartmouth (Dean hurts Sam while training and feels really guilty, also some protective John) The Queen of Light took her Bow (https://www.fanfiction.net/s/4875088/17/The-Queen-of-Light-Took-Her-Bow) is a really well-written fic. I haven't read it in a while but there's definitely hurt!sam and I'm pretty sure John and Dean feel guilty
Like I said, I can only rec gen fics but I hope someone can rec what you're looking for. I hope you like these anyway!
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Date: 2016-08-02 06:16 pm (UTC)Fics where Sam is hurt and John in protective: I'd recommend looking at skagtrendy on ffn (https://www.fanfiction.net/u/1397836/skag-trendy) and Menthol Pixie (ffn (https://www.fanfiction.net/u/18504/Menthol-Pixie) and LJ (http://mentholpixie.livejournal.com/)) who both write a lot of hurt!Sam and John in a positive light, if you have a look through their fics I'm sure you'll find something you like.
Kokoda2007 (https://www.fanfiction.net/u/1303844/kokoda2007) has a lot of hurt!sam with some guilty John and Dean
Also: Wired (https://www.fanfiction.net/s/4264997/1/Wired) by Faye Dartmouth (Dean hurts Sam while training and feels really guilty, also some protective John)
The Queen of Light took her Bow (https://www.fanfiction.net/s/4875088/17/The-Queen-of-Light-Took-Her-Bow) is a really well-written fic. I haven't read it in a while but there's definitely hurt!sam and I'm pretty sure John and Dean feel guilty
Like I said, I can only rec gen fics but I hope someone can rec what you're looking for. I hope you like these anyway!