I would like just the ability to encrypt individual files or folders, rather than File Vault's full home-folder encryption.
While File Vault obviously should prevent an attacker seeing what's in my home folder, in addition to preventing them opening any of it, the lack of true Time Machine support is a bit of a killer for me, as I'm not too fussy about a lot of my files, but some particular folders I would like to secure without the hassle of managing images or scripts myself. A nice "encrypted" checkbox would be brilliant, especially if Lion could also add a better mechanism in Time Machine for incremental backups of an encrypted folder without backing up the whole thing each time.