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http://www.khanacademy.org/
This has Math up to your upper calculus.
Science such as Chemistry, Physics and biology.
Some History
and many more. (Thanks to BRWright for the khan academy suggestion)
Pauls Online Math Notes is one of the best free resources for math study, from personal experience.
Are there any college search engines with a filter for political or religious affiliation?
College Board has a religion filter. You could search US News and see what they come up with.
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