My Mac has an external disk attached, and I often get "disk not ejected properly" warnings after resuming the computer from sleep. These warnings appear only when the disk has spun down during the sleep, and it seems that they are related to how long OS X is willing to wait for a device to become present before declaring it disconnected after resuming from sleep.
It would be nice to not get the annoying pop-up upon resuming from sleep, and the messages about journal replay in kernel.log look slightly alarming, even though it is unlikely that anything wouldn't have gotten written to disk while the computer was idle before going to sleep. Can this wait time be increased somehow?