File transfers over USB cable from computers is unreliable. There are reports that coping files from the phone works ok, but trying to copy files to the phone causes issues. I've tried this both on XP, Vista, and Win7 and had the same issues with intermittant transfers, timing out, and other issues. For example, my ringtones transferred fine, but I couldn't transfer any pictures.

Possible smack myself in the forehead moment. For all those with issues transferring files, try using the USB cable that comes with the unit. I just tried it, and all my transfers worked fine. I have a USB->MicroUSB cable that I leave plugged into my computer to hook up to various devices. Apparently, there was something about this cable the GNex didn't like.

Resolution:
This has been discussed on XDA. The problem has to do with lack of true USB host mode. Or could it just be the cable you are using?
There are a couple of workarounds:

Easiest: Download Airdroid from the market. It lets you wirelessly connect to your phone and control it, including transferring files. Can't believe it's free, works pretty slick (Must use Chrome or Firefox, don't use IE)

Moderate: In CWM, mount USB storage. I'm going to try this to see how well it works.

Wifi bootlooping. Some users report that when connecting back to wifi, it causes bootloops.

Resolution:
No resolution at this time. Possible hardware defect. Lightflow has also been suspected as causing problems.

Some users report that while playing movies in a dark environment, that scenes with black lighting can tend to exhibit blue blocky artifacts.

Resolution: This issue is caused by posterization during the encoding process. While we like to think that black backgrounds are truely black, instead there may be minute amounts of detail that is being transferred. This gets exacerbated when the video is transcoded. Normally, this wouldn't be visible on traditional backlit LCD screens as it would be washed away, but instead, with the super contrast of AMOLED screens, it becomes more visible. It's also being exaggerated by the pentile arrangement of the subpixels, causing the effect to be more pronounced.

Unfortunately, there is no resolution at this time other than using higher quality source material. Some report the app "Screen Adjuster" helps to alleviate the issue.

Some users report extra clicking sounds happening quite a while after doing an operation. There are normal sounds that go with events, like touchscreen input, and abnormal sounds that happen afterwards.

Resolution:
Possible hardware defect, return phone.

Some users reported that the power button acts strangely after rooting.

Resolution:
Pretty much confirmed to be a problem with Lightflow.

Some users reported keyboard lag, especially in landscape mode.

Resolution:
Most likely endemic and hopefully will be fixed by a software update. In the mean time, there are other keyboards available in the market.

Some users report that when using bluetooth headsets, the only app that works with the controls is Google music, other apps get locked out.

Resolution:
No more information at this time.

Some users report very slow speeds when connecting to a computer to transfer files.

Resolution:
From my own experience, I did have this issue once when I plugged it in, it defaulted to USB1 mode, and not USB2. File transfer speeds were miserable. I unplugged and tried again and everything worked fine.

Not sure about the long term resolution.

Some users report getting garbled text, no text, or even random info when trying to use the Voice to text feature, or voice actions.

Resolution:
No more information at this time.