Agreed. I had been running FreeBSD exclusively for well over 5 years before I switched to OS X. I can't say that I miss FreeBSD much. Still love it though, always will!
A lot of people motivate that Linux has got an apt and this makes it a hacker friendly platform. I've started using FreeBSD from 2-RELEASE (sorry, don't remember the numbers). The ports sucked there so much, that you can't even imagine now. But it still was a great platform to develop and to use.
The Darwin' port system is a very nice tool. They're really similar to BSD ports and they are powerful enough. You just never learned how to use it. Do you still miss apt? Get Fink (http://www.finkproject.org). What can be easier?
People, don't get me wrong, I'm not about a holy war. But I'm really confused why guys over here want to have two laptops running Unix at the same time. ;)
Another problem I find is that there seems to be a 'Mac' way of doing things which is different from both linux and unix/bsd methods (e.g. binaries often go into /Library/Framework/... instead of the usual /usr/bin or /usr/local/bin, etc.) which causes problems when interfacing with other *nix tools.
Finally, an unrelated thing (but one that affects me a lot) is the complete lack of the /proc filesystem. I think BSD/Unix doesn't have this either, so perhaps with your background you won't miss this in any case -- but I grew up on Linux and find /proc to be invaluable. It allows for easy programmatic access to processes using only file I/O, as well as allowing for awesome helper programs like htop.