The main difference between Bongo and EMMS 2.0 is that the
former has a more elaborate user interface, while the latter
is more mature and supports more formats (for example, Bongo
cannot yet play radio streams).  It might be fair to say
that Bongo is a GUI that can play media, while EMMS 2.0 is a
media player that can display a GUI — although this
characterization is becoming less and less accurate as the
feature sets of the two players converge.  While Bongo and
EMMS 2.0 do not share any code, both sprung out of the
EMMS community.

In fact, Bongo started out as an experiment in creating a
better “playlist buffer interface” (PBI) for EMMS, which
had traditionally had an all but invisible UI, with the PBI
added pretty much as an afterthought.  (See
[http://lists.gnu.org/archive/html/emms-help/2005-08/msg00057.html
this thread] for the start of EMMS 2.0 and Bongo.)  The
experiment quickly got out of hand as Bongo evolved into a
complete media player in its own right and DanielBrockman
started to use it full-time.  In response to this,
JorgenSchaefer, the original author of EMMS, — who had
always thought that the very concept of a PBI was
unnecessary and lame, — quipped, “Great, he took the worst
hack of EMMS, and made it into a new player.”

For a while, the intention was to eventually merge Bongo
into EMMS 2.0.  However, this plan was pretty much floating
around on ice, and it shot right off into space when
YoniRabkinKatzenell stepped up to rewrite the EMMS PBI for
EMMS 2.0.