Brute force work efforts like password cracking tend to be an exponential times a constant -- say, 2^32 operations that take 100ms each. Increasing the complexity of a legitimate password verification increases the constant. Interestingly, the more efficient a legitimate verifier becomes, the more efficient your brute forcer is.The algorithm is far more complicated than "raw" MD5. It consists of 1000 iterations of MD5 with both output from the previous iteration and the original input (plaintext password and salt) being rolled into the hash on each iteration.
Not that brute force is the only approach available. There are numerous attacks that might break "pure" MD5 but fail given such massive overlapping. There are, however, others that abuse extra rounds to great effect. For instance, SHA-0 is an 80 round algorithm. Biham's paper (http://eprint.iacr.org/2004/146/) showed that an 82 round variant is actually much weaker. And Joux's unreleased paper makes it very clear that simply stacking primitives doesn't create nearly the level of combinatorial complexity that you'd expect.
Of course, as I've said elsewhere passwords really aren't at all vulnerable to the MD5 attack. But, if they were, extra iterations wouldn't be helpful. Once the first round collided, all future rounds would continue to collide.
--Dan www.doxpara.com