BCrypt vs Key Stretching MD5
Any time there is a choice and password search is an issue, one should prefer scrypt or perhaps bcrypt to stretched-md5, or even PBKDF2.

The reason is that scrypt and bcrypt provide better security, by requiring a bigger investment in hardware (in particular, RAM) for the would-be password cracker, assuming parametrization yielding the same runtime for legitimate use. If enough RAM is available in legitimate use, the additional security obtained by using scrypt can be quite dramatic. See the following table from the paper Stronger Key Derivation via Sequential Memory-Hard Functions defining the Scrypt Password-Based Key Derivation Function.