I don't use either java or any browser plugins (other than portable Firefox plugins) so I haven't come across that yet. I used freebsd for a desktop for 6 years, replacing Solaris and not once did I use Linux compat as well.
It got shot in favour of windows because TBH that pays the bills better at the moment.
FreeBSD however runs a lot of the hidden glue at our company.
A big part of that is the state of the linux emulation. While it's solid technically, the linux it's based on is ancient... the NEW linux base that is being phased in is based on CentOS 6, which is already over 3 years old. The CURRENT linux base is Fedora 10, which is 6 years old. Both of these are so old that compatibility with proprietary software are limited.