I'm not going to put much effort into this list.
-While playing Resistance, shooting all the Chimera...and suddenly Nathan Hale is walking to a wall shooting in the air. This lasts for several seconds.
-There are times when users almost need to look up the instructions to do something as simple as set the resolution. It's not always obvious where options are located or that pressing a direction instead of a button is needed to proceed further into the menu.
-The action buttons are not marked in the menus. i.e. attaching a memory card...going to the utility for it doesn't say anything. You need to magically know to press triangle in order to get to the copy files menu
-The PS3 doesn't automatically detect new video connections when booted. You can't just plug in an HDMI cable after you've been using analog...you have to set it up through your old connection first
-The system doesn't automatically update (after being told an update is needed)
-The system settings menus are confusing
-PSN registration is a long arduous process
-Updates take a dozen button presses, connecting the usb cable, and a lot of time.
-Exiting a game shuts off the controller.
-Text entry sucks. Keyboard isn't optional to be effective.
-Users can't even lightly drop the controller on the couch when watching a movie or else it will hit the triggers...causing fast forward/rewind
-Blu-ray is nothing to write home about. Without really good vision, or a Masters in obsessive detail scrutiny, it's difficult to tell the difference. It's even more difficult to tell the difference when the movies are in motion.
-PS3 Linux does not have GPU support which means no real gaming. Switching between the PS-OS and Linux would get annoying after a while (have to enter a command on boot to swap OS's...then reboot). Linux should be run in a virtual machine as opposed to directly off the hardware.
-Graphics aren't really showing. The 360 is putting it to shame (because it's over the "lesser" component cables) for most games at this time.
Updated 04/03/2007: Added some information per comments.