How do I associate a custom post type with another through a taxonomy or storing an ID in a custom field?

I’m working this problem discussed here: Custom Comment Types, but I need more clues to map out the process. I want to create custom post types and associations between Questions & Answers, and Pin-ups & Critiques. I think that I want to do this because I want to be able to archive and create feeds for Answers and Critiques separate from Post Comments For example, for a given author/user home page, I want to be able to list Questions posed, Answers given, work Pinned-up for comment, and Critiques made. An Answer would include the title of the Question it refers to. This is more of an aside, but I am imagining a role/capability to comment on each custom post type (Question, Answer, etc. ala Quora and Stack Exchange). The comment referenced 2 options: using a custom taxonomy and storing an ID in a custom field. I’m self-learning, so any additional help is appreciated.