PhilC

The only DL partner that flies to Quito is Continental. As an alternative to Quito, you can also fly CO to Guayaquil. The only carriers that fly from mainland Ecuador to the Galapagos islands are TAME and another Ecuadorian airline. The flight from Quito to the Galapagos (either San Cristobal or Baltra) stops and picks up/drops off passengers in Guayaquil both directions so it takes about 3-3.5 hours. The flight from Guayaquil takes about 1.5 hours but I think Quito makes a more interesting stopover.

Edited to add: It's possible you could also fly Avianca to Quito or Guayaquil, but you would have to route through Bogota.