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This has been discussed time and time again. Threads like this typically end up in a Auto Vs. Manual Pissing contest.
In all seriousness, your question is too vague. As I read it the appropriate answer is "yes, the most obvious differences are as follows: manual has three pedals, you have to change the gears." I doubt that's what your looking for...so search using keywords that your curious of, if you can't find anything then post those questions.