Ben Bolker's book is awesome.
Gelman and Hill's Data analysis using regression and multilevel/hierarchical models textbook has been an invaluable resource for my applied work. I found the writing very intuitive.
Bayesian Data Analysis is a monster tome. I've read up to nonlinear models and it has been an incredible journey.
Stan manual is secretly the best applied stats book in existence. I couldn't do what I do without it.
Elements of statistical learning is a very interesting read. I've gotten a lot out of the section on model checking and validation. This book and BDA are more similar than you'd expect.
Bapst's handouts are excellent high-level overview of the math and motivation of PCMs.
The phylogenetic mixed effects model papers, Lynch 1991 Evolution and Housworth et al., 2004 Am Nat, are fantastic and are the perfect connection between PCMs and hierarchical models from Gelman and Hill and BDA. Ives and Helmus 2011 Ecological Monographs serves a similar purpose with a more applied bent.