My preference is GNU/Linux for three reasons.
1) I like the functionality in the GNU versions of the standard UNIX
utilities.
2) The variety of distributions from which to chose. I really like
Gentoo because of the level at which you can customize your system.
3) It's free software and promotes copyleft.

I regularly use Solaris because that's the system on which I do most of
my job. ZFS does a good job of handling very large files systems and
files.

I also use Cygwin because it gives me UNIX on my XP machine at work.
It's great for those who can't live without their UNIX utilities.

I also use AIX at work but it seems to lack a lot of the utilities and
options that are commonly found on Linux. This may just be a problem
with the default installation.

I've used FreeBSD in the past and it works great. I really like Ports
package management.