See https://bitcointalk.org/index.php?topic=72022: I am interested in inserting sha256sum data into the block chain.

I see that the protocol you currently use has the following message types:
'01' for md5
'02' for ascii

May I suggest to add the following?:
'03' for sha256sum

I see you already have an option for md5sum, but from what I know, the MD5 algorithm has serious security flaws, so it shouldn't be used as secure hash algorithm. SHA256 is used by Bitcoin itself, so using anything that is better than SHA256 doesn't make sense, until Bitcoin itself switches to a better hash type. Since a SHA256 hash is still quite small (256 bits = 32 bytes = 17(?) payments using your scheme), I don't see a reason to use smaller hashes either. So IMO SHA256 is the "best" secure hashing function for Bitcoin messaging.