I love Ann Dee Ellis's books - I think she is amazing -
THIS IS WHAT I DID (bullying, abuse, guilt)
EVERYTHING IS FINE (sibling death, parental depression, abandonment...)
my most favorite serious subject MG book is WHAT JAMIE SAW
I also love some books that were already mentioned TROUBLE WITH HALF A MOON and WAYS TO LIVE FOREVER
TALL STORY by Candy Gourlay is on the surface about a girl who wants to join the basketball team and who is embarrassed by her older half brother with who has a medical condition -but it is also about immigration, identity and family.
OLIVE'S OCEAN by Kevin Henkes (death)
LOVE RUBY LAVENDER by Deborah Wiles (other books by her too)
Maybe a reference could be
www.SeriousSubjects.com - it is out of date (sorry) but has books from YA to pb, fiction and nonfiction arranged by subjects
Also, my debut THE END OF THE LINE is about a boy coping with his role in the death of his friend and his uncle is serving in Iraq.