Plugin to do code syntax highlighting w/ tool-tips & links ?

I would like to find a way to use a code syntax highlighter and allow for sections of the text to have tool-tips and links; the following link is an example of the behavior I would like: http://serversetup.global-domain.com/operating-systems/centos/setup/
I use the site for keeping notes on servers I setup (personal and work) and figured the info might be useful to others so I’ve started cleaning it up and adding info/tool-tips/man pages like the above. All the other pages are currently private since they aren’t marked up, I’ll make them public when I can format them like above…
I’ve tried various combinations of syntax highlighters and tool-tip plugins but I always run into the same problem; the tool-tip short-code or html gets printed on the page instead of working as a tool-tip (same with links on non-url text) or doesn’t show up and doesn’t work either. Oh, even though the above page doesn’t contain any “code” per-say, other pages do, including bash, php, config files and more which is why I was looking for a syntax highlighter…
Any suggestions on a plugin or combination of plugins that will do this?