What kind of black/white/gray box tests can I conduct on operating systems on servers?

I'm about to get started on doing some penetration tests on a couple of servers and I did some advanced reading on the main categories of tests I can conduct:

1. Kernel
2. Memory
3. File IO
4. System Configuration

Are these right? But what I was really wondering is how exactly should black box penetration tests be carried out in those categories above? The only ones I can think of at the moment are like DOS, or MITM.