Donors Choose is a pretty cool website, you donate to teachers in classrooms that need supplies and stuff. They will send you pictures and stuff so you can feel the difference. Funded some elementary school science class, they were all pumped up to do some experiments.
http://www.donorschoose.org/
Vitanna is a similar website, but funds people's educations around the world. Takes some guy or gal that's trying to get a higher education in order to break the cycle of poverty and provide for their families better. The best part is, it's a loan, so once they finish classes and get a job they pay you back, and you can donate to others. I put $100 in there, and have had it returned many times over.
http://www.vittana.org/
Last one is Pencils of Promise. Real small group that has grown from $25 to millions of dollars raised mostly from donations from school kids, spare change, etc. They work with 3rd world villages to build schools, but keep them involved with construction, teaching, etc so that the villages really have a vested interest in the success of their kids.
http://www.pencilsofpromise.org/
All three of these I chose because #1 I can see exactly where my money is going and who it's helping rather than into a large organization like Red Cross, etc. #2 the people that this is helping are all trying their best already and just need a hand, not a freebie. #3 the world needs more education, you'd be surprised that people on this forum are actually well educated compared to most of the world. Change the next generation to hopefully be better than us.