Here is a list of some charities I support or am considering supporting in the near future.

Project A.L.S.
In response to the ALS Ice Bucket Challenge, I pledged $20/mo for a year to research for a cure to A.L.S. This organization has the best program funding rate of their competitors.
Michael J. Fox Foundation
Funding research into a cure for Parkinson's disease. They boast an 89% program funding rate and high fundraising efficiency.
Moore Youth and Family Services by way of United Way of Central Oklahoma
Local organization that provides counseling and other services to community members in need.
Parsemus Foundation
Vaselgel Project — The non-profit Parsemus Foundation is trying to get Vaselgel approved and on the market in the United States. This revolutionary form of male contraception is long overdue.
Oklahoma City Community College Foundation
Provides scholarships to local students, specifically marked for students in science, math, and engineering disciplines.
Wikimedia manages the renowned Wikipedia and a number of other projects to facilitate the free and open transfer of knowledge. Regardless of your stance on the quality of that information, facilitating learning throughout the world is unquestionably a worthy endeavor.
Kiva itself is a 501(c)(3) charity that facilitates microloans around the world, specifically in under-developed nations. I tend to select loans that facilitate agriculture and small business but there are a lot of options. I plan to continue my current contribution rate until I build a large enough portfolio to allow continued reinvestment of repayed loans, then I'll reduce how much I add in new loans every month. At any rate, Kiva lets you help the third world get more developed, like a charity, but through capitalistic means.
(Join Kiva) (My Lender Profile)
Project Gutenberg
Project Gutenberg works to take works that have come into the public domain and make them available to everyone for free to read without complication. They rely heavily on volunteers for labor but servers and bandwidth still cost money. Operating continuously since 1971, they now have over 45,000 eBooks available for download in a variety of formats from plaintext (they're all available in plaintext as a baseline) to Kindle.
Project Gutenberg is a 501(c)(3) charity and all donations are tax deductible in the U.S.
Extending the mission of Project Gutenberg, LibriVox aims "to make all books in the public domain available, for free, in audio format on the internet." They draw on Gutenberg as a source for their texts and also rely on volunteers for most of their work.
LibriVox operates under the umbrella of, the Internet Archive. As such, all donations run through them and are tax deductible in the US.
(Donate), the Internet Archive
The Internet Archive has been around since 1996 with the aim of building a library for the Internet. Their stated mission is to provide universal access to all knowledge, a goal with which I can certainly sympathize. They work to provide free access to curated archives of text, audio, moving pictures, software, and snapshots of web pages.
The Internet Archive is a 501(c)(3) charity and all donations are tax deductible in the U.S.

Artists and other Content Producers

They aren't charities, but I also act as patron of several online content producers.

WoodWorking for Mere Mortals by Steve Ramsey
Steve makes accessible work-working videos and often does fundraising for Make-A-Wish Foundation.
C.G.P. Grey
"Complex things explained"
Crash Course
The brothers Green bring us a series of videos teaching U.S. history, chemistry, world history, biology, literature, and ecology.
Hank Green and Co. bring regular episodes discussing science news, history, and concepts.
Minute Physics
Physical concepts taught in an accessible manner as narration over whiteboard animation.
Applied Science
Excellent engineering/explanation/experimentation videos spanning a variety of topics.
Danielle Ate the Sandwich
Ukelele, guitar, singer, and song-writer. Danielle has it all!
Quirky, interesting originals and covers. Jack Conte and Nataly Dawn play all the instruments.
Julien Neel (Trudbol)
Keeping the art of barbershop quartet alive on YouTube.
Sonny Vande Putte (SgtSonny)
One-man quartet videos, like Trudbol, and sometimes in collaboration.
Saturday Morning Breakfast Cereal
Zach Weinersmith draws five days a week to entertain you on philosophy, science, religion, and everything in between.

If you like, you can see my profile pages on Patreon and KickStarter.