/usr/local/include/wx-2.9/wx/buffer.h:42: undefined reference to `wxTheAssertHandler'
obj/nogui/init.o(.gnu.linkonce.t._ZNK13wxArrayString4ItemEm+0x45): In function `wxArrayString::Item(unsigned long) const':
/usr/src/bitcoin/trunk/uint256.h:526: undefined reference to `wxOnAssert(char const*, int, char const*, char const*, wchar_t const*)'
Those are probably due to switching to the release build of wxWidgets instead of debug. They're moving towards only debug build and ditching the release build, so they probably don't care that their release build is broken by referring to non-existent assert stuff. There's nothing to fear about the debug build. It's fully suitable for releases.
bitcoind runs as a daemon and can either be controlled by command line or JSON-RPC.
Thanks madhatter and generica for detailing the instructions for building on freebsd.