It's funny you mentioned processes entering a quasi-paused SIGSTOP-ish state. I swear I've been having tons of problems with Java/Tomcat the past week or so I've been on 10.12.1 (betas), and I keep thinking I broke my config by updating my Java version, changing my Tomcat config, or some other "system configuration entropy"! Nice to know I'm not alone and that I'm probably not crazy.

Tomcat 7.0.72 from Homebrew, Oracle Java 8u112, PostgreSQL 9.3 and 9.5.