Comment data structures, not code
I believe that if your code requires a significant amount of comments to understand it chances are that it is poorly written code. The underlying <B>data structures</B>, however, should have copious amounts of comments about their structure, model and most importantly any <B>assumptions</B> they make. The assumptions are the hardest part, of couse, because the problem with something you take for granted is that you are not aware that you are taking it for granted.
file format of DSA keys
OpenSSH uses PEM format for DSA key files which is incompatible with the SSH2 key file format. So far I couldn't get OpenSSH to authenticate with a DSA key to an ssh2 server because of this. I can't put the public key generated with OpenSSH on the ssh2 server and I can't get OpenSSH to use a private key generated with ssh-keygen2.