Update on acquiring an ECC (November 2013), all based on my own experience with this recently:
Unless the rules have changed again, the ground situation surrounding the issuing of the Emigration Clearance Certificate (ECC) appear different than set out above, at least for me:
1) Suboffices do issue ECCs. It was issued to me by the immigration suboffice in Legazpi, in November 2013.
2) Validity seems to be 1 week; the Legazpi office issued it on November 12, with my departure date being the 18th (visa expiry); likewise, the Intramuros office in Manila had told me earlier that (if applying for it there), 'I should come there to apply for and get it 1 week before my departure; so I believe the validity is 1 week (not more! don't plan to get the ECC and then fly 2 weeks later, it could get you into trouble).
They indeed don't seem to issue ECCs at airport immigration anymore. At least not when I tried to get through without one in October at NAIA - I was turned back; I pleaded, was ready to pay a fine or whatever, but they wouldn't budge; it happened on a Friday, and I was directed to go to the main Intramuros office; upon arrival there and submitting the ECC application, they told me, after letting me wait, to come back the following Monday as they 'had too many applications to process'. And oh, Sir, if you come back on Monday, your visa will have expired, so please file for an extension on Monday first and pay the fine (my visa expired that Friday)...with the prospect of a weekend in a Manila hotel and another (Monday) morning in a nightmarishly crowded Intramuros office, not to mention the uncertainty of being able to quickly book a new, reasonably priced flight out of the country at such short notice, I asked them if I could go back to Legazpi and do the extension and ECC application in the (for me more familiar) suboffice there. They said I could and that turned out to be correct. The rest is history...
Being turned back at Naia immigration was a humbling experience, with a lot of stress as a result; then the financial setback: I lost my flight tickets (non-refundable), my hotel and other advance bookings abroad, had huge extra travel expenses, totalling near php 20,000.
Note: In Legazpi, I paid Php 500 for the ECC, but was also asked to get the original application papers (submitted at Intramuros) notarized by a local notary, which set me back another 500 (a rip-off, the standard fee is 250);
So my advice is to talk to your local immigration suboffice and get it all arranged well ahead of time...
All the best.
M.