What Trusted Root Certification Authorities should I trust?

If I had a MITM rogue cert on my machine, how would I even know?

You often wouldn't. In fact, this is often how SysAdmins snoop the HTTPS sessions of employees: they quietly push out a trusted cert to all desktops, and that trusted cert allows an intermediate proxy to MITM scan content without alerting the end users. (Look up "push out CA for https proxy group policy" - ran out of links with my low reputation!)

Does a list of "accepted" certs exist?

There are a few, generally the default list of certs on stock operating system installations. However, there are ALSO hardcoded lists of CAs in certain browsers (e.g., http://mxr.mozilla.org/mozilla-central/source/security/certverifier/ExtendedValidation.cpp) to support Extended Validation ("green bars"), but EV lists also vary (e.g., http://www.digicert.com/ssl-support/code-to-enable-green-bar.htm)

Am I safe in removing the expired CAs?

Generally, yes...if all you're doing is surfing web sites. However, you may run into other issues running certain signing applications.

Can I know if/when I have ever used a CA for HTTPS?

Hmmmm...sounds like an app that needs a-writing. ;)