When GNOME Keyring, needs a password to add an SSH key to the agent, it pops up a system modal prompt to get the password from you. I use KeePass, so this means that if I forgot to copy the password before the SSH attempt, I'm out of luck because of the system modal behaviour, and have to fail the connection.
See also this GNOME bug. As of GNOME 3.18, the workaround provided there isn't valid.
Since I would prefer to not muck around in GNOME's source code: is there any way, via configuration, to make the system modal prompts not be system modal?