Niche pieces of software are absent; valgrind for FreeBSD is a fork that doesn't support amd64 last time I checked.
There are less people out there running the exact same application binary + underlying OS as you, which means you're less likely to find people who've had (and solved) the same issue as you.
Using it for your desktop is a bit masochistic. Widespread virtualisation means this isn't really an issue anymore - you can have a VM that mirrors your production setup.
We're still using FreeBSD and aren't likely to change anytime soon. I agree with everything aristus said.
And if you need something special and/or exotic it isn't really that hard to build from scratch. I can guarantee 90% of the dependencies can be installed as a pre-built package.
Pros Stability & performance are noticeably better. BSD's virtual memory system doesn't leave tons of pages in the Inactive bucket. The TCP stack is the best of class, and the UFS2 filesystem rocks the house. Jails have been in BSD more than a decade and don't waste so much $#$@ memory compared to virtual systems. Performance under heavy load is much much better.
Cons: SMP and 64-bit support. :( Linux is the Golden Child for new hardware, so BSD lags behind. I remember panicking my 5.1 kernel with a USB drive, as late as 2004.
Joyent have a good reputation but I'm not a fan of Solaris ancient userspace tools - something as simple as checking the size of a disk is made complex by Solaris not bothering to include an 'h' option - so you have to count your terabytes of disk in kilobytes.
The Solaris filesystem layout is non-FHS and a rather odd mess, with binaries in var and etc, and variable files in usr.
People often complain about Ports but you soon get used to it and I've found the port maintainers to be helpful on the odd occasion when there has been a problem.
Although hardware support can be said to be weak, when choosing servers there aren't a lot of chip sets out there so things are mostly covered. Certainly when deploying to HP or Dell boxes I have had no problems. It only takes a few minutes to check h/w compatibility lists. Chosing the correct servers for any job requires careful research anyway.
The most annoying thing is explaining to people that although it's open, it's not Linux and yes it is production ready.
Anyone have any thoughts on Linux v BSD security?