Noah -- To start with, I recommend looking at www.tripprep.com Secondly, since you're in Toronto, you've got an excellent department of travel medicine at Toronto General Hospital. That group is lead by Dr. Jay Keystone, one of leaders of the travel medicine speciality. Here's his info: Keystone, Jay S., MD FRCPC MSc (CTM)
Centre for Travel and Tropical Medicine
Toronto General Hospital, 200 Elizabeth Street, EN g-208, Toronto, Ontario M5G 2C4
Canada, Telephone: (pre-travel appointments): ++1-416-340-3000,(post-travel): ++1-416-340-3675; Fax: ++1-416-595-5826.

Some general info: Mefloquine is the CDC recommended anti-malaria for Ecudaor, although as others have stated doxy can be used. No need to worry about Malaria in the Galapagos or the Andes highlands, but pretty much present anywhere else at altitudes <1500m. Depending on your past medical history one may not be indicated for you. The best protection from exposure is to not get bitten in the first place... dusk to dawn is the time for the bites. Again, you should use Permethrin impregnated bug netting, and an insect repeallant high in DEET - say 20% or higher. Those herbal repellants have been studied and do not work.

Boil it, cook it, peel it, or forget it. Sure you know to watch the food, and water. Not all pumps and filters are good-- check to see the smallest filtratable material.. some just don't go low enough.

Other recommendations: Hep A -- highly recommend it, Hep B -- depends on "risky" behavior, might be better for SE Asia , make sure your tetnus is up to day - within the last 10 years. Just know proof of Yellow Fever vacination is required if previsouly traveling or transiting (except airport) an endemic area within the last 6 days.

If you need more detailed info, feel free to contact me.