I have a couple of favorites.
1. Remote Area Medical provides free health, vision and dental services (and veterinary when possible) to uninsured and underinsured residents in mostly rural areas. Medical caregivers are volunteer and program costs are low.
I was fortunate to volunteer once at one of their clinics and saw life-changing differences made in people's lives.
They're not big enough to be rated on Charity Navigator.
Remote Area Medical - Wikipedia
Segment from 2008 on 60 Minutes:
Remote Area Medical - part 1 - YouTube
2. I also like Donor's Choose which allows you to directly fund various classroom projects. It's been given Charity Navigator’s highest rating every year since 2005.
From Wikipedia: "DonorsChoose.org enables teachers to request materials and resources for their classrooms and makes these project requests available to individual donors through its website. Donors can give $1 or more to projects that interest them, which are searchable by school name, teacher name, location, school subject, material, and keywords. DonorsChoose.org then purchases the supplies and ships them directly to the schools. Every project contains a line-item budget and a description of the project. All donors receive photographs of the project taking place in the classroom and a letter from the teacher."