Well, here are my two cents worth on this topic.
 
When I returned from the Philippines in early December last year I had been
forewarned.  So I dutifully went, at the Cebu International Airport and before
checking in, to the little window named something like "Games and Fisheries
Department" to buy an export fishery license for my shells.  I understand they
have offices in every international airport; you don't have to get anything in
advance from Quezon.  Anyway, the license cost the equivalence of about $0.35
(yes, 35 cents), but it takes some time to prepare it (the paperwork already
mentioned); I would advise to allot some extra time for this endeavor.  I was
actually already in the check-in line when the fisheries person came running
with my license, very nice and helpful.  HOWEVER:  It was that same fisheries
department clerk who, when I asked for the license originally, went through my
whole shell suitcase, opening and checking not all but many boxes all over, and
making a general mess out of things.  He of course was looking for the
'fobidden' species already mentioned, so he opened all the larger boxes, but it
was overall quite a thorough search.  Only when he was satisfied that none of
the 'no-nos' were in my suitcase, he finally started the paperwork for the
license.
 
A friend who also went through the same procedure at the same airport sometime
in the summer of 1998, though, got the license without any fuss and no checking
of luggage at all.  So it seems to depend on who you're dealing with -- or
perhaps I just look untrustworthy???  In any case, don't try to 'smuggle'
anything out, get your license, and be sure you start the process on time so
that you don't miss your flight.  The whole thing may take an extra 45 minutes
or so.
 
But if you're lucky enough to go there in the first place, who cares about a
little taste of bureaucracy at the airport, right?  In any case, enjoy!!
 
Monika in New England, USA