Being several years out from my CS degree, I'll give my opinions on how useful each of these would have been.
- study and practice for certifications
- is CompTIA Linux+ a good beginner certification? Server+?
I've never thought much of certifications, and most of what I've seen on SO indicates similar skepticism of their usefulness. I'd say no.
Straight out no from me on this one. As I understand, it's just a GUI version of what they should be able to do from the command line, which, IMO, is much more important for anyone going into computer fields.
Installation and simple configuration are trivial, but you could go into some advanced Apache configuration, maybe a day or two on rewrite rules. Actual PHP code should be saved for a PHP/web class.
This could be useful. I've spent a good deal of time on trying to figure out how to get a mail server running and properly configured. A very practical topic, I'd suggest fitting this in. Preferably with as much of the underlying principles of email as you can fit in.
Like the above, highly recommended. Might be quicker and easier to explain the underlying principles than the mail server.
This too would be good, though a lower priority than email and DNS. But I'm afraid I can't offer much in the way of suggestions on the particular software to use.