The boss wants to dump everything into one server so they can remove
the file server but I am assuming that it will be more secure if we
can keep things separate.
It's definitely better to keep services on separate machines, but if paring down to a single physical box is what you have to do, then maybe virtualisation is the way to go.
Without knowing why the boss wants to get rid of the other fileserver, it's hard to know if that will solve your problem, but it's definitely worth looking at.
By doing this, you could set up 3 different virtual machines, one for the intranet, one for the fileserver and one for the app server. Each would appear to be a completely different computer, but they all share the same physical resources.
There's a bunch of different virtualisation programs available. I'm most familiar with VmWare, but there's also Xen from Redhat and even Parallels which you already have.
