I was just thinking about password cracking and specifically about that program that cracks windows hashes in under a minute...rainbow crack. Now is it possible to convert other hashes (MD5 for example) into a windows hash, and will the program still be able to crack them. If that would not work..why not?

why not generate a rainbow table for md5/sha1 algorithm in order to crack your MD5 hashes? RainbowCrack can do this, read the documentation. I'm not sure about the conversion but I think it's impossible.

no, you can not convert hashes (unless first knowing the plain text value)... it just doesn't work like that (not to my knowledge at least)... you hash a hash maybe twice with the same cipher or multiple ciphers, but you can't convert one hash directly into another...