I just had a Twilight Zone experience! I was just setting up ssh on my desktop machine and got the wrong path in the -i parameter (identity file) my server is set for "PermitRootLogin without-password", which as I under stand it disables the password login only. I did NOT get the pass phrase prompt and got error message to the effect of key file not found.
and then I got a functional ssh connection to my server!

I had previously been using PUTTY and it too would connect without an identify file!!!!!!!

After a bit of panic a reboot of my DESKTOP machine that I was running the ssh client on the problem went away???. (The server was NOT rebooted although it had been rebooted the day before)

I gotta wonder if I have been compromised -- does anybody have any idea whats going on???

I know that PUTTY has a mechanism to remember identity files and log you in automatically without needing passwords but I had not run it, and why would it also affect ssh???

Posting lines, from the server, wherever SSH logs to and sshd_config (as in 'grep ^# /path/to/file|grep .;') and from the client your botched command line and your ~/.ssh/config may shed a light on things. Apart from that root shouldn't be allowed login over any network so you're not adhering to best practices regardless of your question. If this is a remote server I strongly suggest you correct that before doing anything else.

As far as detecting compromised binaries: your distribution (which?) may or may not have package management tools to help you. If it doesn't and if you haven't set up file integrity checking (Samhain, Aide or even tripwire) then compare package contents with a known good package downloaded from a trusted repository?

End of panic attack.

Apparently gnome_keyring daemon runs by default in Ubuntu. It also appears to work with putty. I sure don't mind computers being helpful, but it sure would be nice if they'd let you know when THEY are helping , , , as opposed to a hacker. what threw me was that it was working with putty and I knew that I wasn't using pageant!