One of the best travel agencies I ever dealt with set up my Ecuador/Galapagos/Peru trip.

www.galapagosholidays.com

The agent knew the specifics of each boat traveling around the island, hotels at each stop, and had long established contacts with local tour guides and companies. They set things up perfectly for me, transfers, flights to the islands, etc. We chatted, they got a feeling for the type of trip and accommodations I wanted, and even recommended sights I would have been foolish to miss.