In using oneswarm I've come upon a few security issues mainly based around the possibility of someone gaining access to your or your friends computer against your wishes. I'll try to keep on the reasonable side of paranoid :-P
1. Ability to install OneSwarm on another partition. As far as I can tell, you cannot choose to install OneSwarm anywhere else than c:\, right? So even if you have the actual data that you're sharing on for example a Truecrypt partition, the information about what you are sharing would still be on the unencrypted system partion (unless you use full system encryption of course). If you could just install OneSwarm anywhere and keep the files that reveal what you are sharing in that location you would have the option of creating an encrypted partion that required a password to mount.
2. Don't save chat history. Say you recommend a friend that politically sensitive Obama speech (LOL!) through the OneSwarm chat. Anyone that looks at his/hers computer can see that you recommended it in the chat history. Since I cannot imagine people will have very memorable conversations through the OneSwarm chat, wouldn't it be more reasonable to not store chat history between OneSwarm restarts?
3. Option of password protection. This is sort of an alternative to 1, why not use the encryption in the program to encrypt all files that reveal what you are sharing and give users the option of requiring a password at startup of OneSwarm to decrypt them?
4. Limited until password. I trust my friends but I don't trust everyone that may be at one of their parties. So why not an option to appear as a limited friend until a password is entered?
4. An option to autostart without Web UI on Windows startup. Not a security issue but really, this should have been implemented in version 0.0001 :-P