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For 128 bit hash method, there are several choices like, md5 and murmur3, which is the best?

Adam Lee
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From the security perspective they are all bad because 128 bit is nowadays much too short.

Therefore you want a cryptographically secure hash take e.g. RIPEMD-160 (which is AFAIR not as much broken as SHA-1).

If don't need real security it doesn't matter if you use md5 or murmur3 or whatever 128 bit hash.

Robert
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    Much too short is exaggerating the matter a bit, brute forcing a 128 bit collision is still pretty hard, and brute-forcing a 128 pre-image is practically impossible. Still I'd use a 160+ bit hashfunction if collision resistance is required. – CodesInChaos Jan 13 '12 at 15:33