Most alternative therapies rely on natural substances - foods. The FDA does not regulate foods the way that they regulate the drug industry. There are no double blind studies showing LD50 (lethal dose 50 - that is the dose of a drug or radiation that is required to kill half the tested population) because in general, foods are not viewed as being that toxic. Therefore you must look at the Science that does exist behind the substance and ask yourself "given what we know scientifically about this substance or method, does it make sense that it could produce the sought after results?" That, and you must rely largely on anecdotal evidence. While it is possible to believe that a pill has cured your headache, seeing cancer go into remission could hardly be considered a placebo effect. You look at the final outcomes of the protocol. If somebody has changed only one thing about what they are doing and they receive a positive result, then you know that that one thing must be having a positive effect.
I hope that helps to answer you question somewhat.