Take all of these video settings with a grain of salt. There should be separate threads for the 47"/55" and 60" since they're different backlight technologies, but everyone is lumping settings together. That could confuse those who don't know better. Someone else's settings may get you close, but aren't necessarily the same on your set - even of the same screen size/technology.
In fact, it appears that some settings look quite differently on various sets. Some users are quite happy with manual settings, others prefer the WOW or AVS calibration discs, and others prefer the calibration settings with minor tweaks. Much of it comes down to personal preference and the variation from set to set.
I won't bother posting my software version as they're different in the USA, but it is the most current available in Australia. I've noticed no difference to anything from any software version, other than now the menu pops up from the remote a bit differently. It used to pause and load the entire screen at once. Now it tends to load some sections before others.
I still feel that the remote is one of the better features, as I use the voice command often. Again, user preference. I've sold my Harmony One as I no longer need it. Only using the Quick remote, mouse and keyboard.
Time Machine also works flawlessly in AU, shame that doesn't seem to be the case in the USA.
My room is dark or medium, never bright. I posted my settings for my 55" on page 28. After calibrating with Disney's WOW Blu-ray disc, I went right back to manual settings as the WOW calibration left a very "bland" picture - whites became light greys and colors looked faded. I've never had flash lighting (which may be specific to the 60" sets). I have no motion blur (Tru-Motion/User settings at 3-3, but anything different on either setting creates from small to drastic amounts). I have no lip sinc issues. I have 0 overrun on 16:9 nor on Just Scan resolutions, which probably has to do with PAL in Australia, rather than NTSC in the USA. I watched much of the Winter Olympics and noticed no issues at all with color variations or vertical lines. I've not had the urge to chance any settings since dialing it in months ago. I've had none of the issues mentioned by others on this thread, other than the apps/internet are terrible (which I don't use anyway).
I don't have a set top box, just a Blu-ray player connected through HDMI, PS3 through HDMI, my PC through HDMI, and digital free to air through the antenna. The PC has movie, TV shows, and scheduling hard drives attached through E-SATA. 90% of my usage is through the PC (XMBC for TV and most sports, browsers for the internet and NFL Game Pass, and KMPlayer for saved movies/TV shows). The other 10% of usage is split between Blu-ray player and free to air TV.
The only benefit I've noticed for Game mode is a bit less delay on the PS3 controller. It has limited options for video settings which make it unattractive to me - doesn't improve online gaming response at all. I've found that a little Kentucky windage (press and release the buttons sooner than normal by a fraction of a second) with the PS3 controller works just as well, allowing me to stay on Standard/User defined settings most of the time. Occasionally I change to Game mode for NCAA and NBA PS3 games as they can be finicky with any lag to the controller.
So I believe I got very lucky with my set (so far, and knock on wood). Too bad that not everyone has enjoyed the same luck, as this is a great TV when it all works.
Hope this helps someone.