You can make Advanced Dining Reservations for all of the Disney owned sit down restaurants.  There are a few restaurants at Downtown Disney that are not owned and operated by Disney like Rainforest Cafe.  This restaurant does take reservations if you call the restaurant directly.  However, most guests tend to stop by this restaurant after shopping around the Marketplace and do not have a reservation.  Before giving up with the 60-90 minute waits, check the outdoor seating area.  There are quite a few tables that are outside of this restaurant right along the lake.  It is a beautiful view and is a nice area to sit year round.  They have heaters during the winter months and fans during the summer months.  It is a nice area to seat year round.  The extra nice perk is the outdoor seating is separate for the regular seating.  If you are told there is a long wait, ask if the outdoor seating is open.  You can usually walk over the outdoor seating and be seated immediately or at the next available table.  It is a great way to save time waiting to eat!