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Long exposure NR is a bit different to normal NR.
Normal NR, software scans the image and picks out pixels that aren't coloured they way they should be ('should be' is based on what the pixels around them look like).
Long exposure NR is different, as neuro said, the camera takes two photos, one normal one with shutter open, one with the shutter closed. the one with the shutter closed is what the sensor 'sees' all the time, ie where there's noise anyway. So by subtracting that from the normal image, it gets rid of the noise that is always present (like dead-pixels, at least in theory).
Basically, it's always a good thing to have Long Exp NR on all the time (it only happens above 1-second exposures anyway), it's always on on my 7D.
The only times I turn it off are:
- when you're capturing action (not that you'd really capture action with 1-second or longer exposures).
- you're impatient (or your better half is impatient, or it's just freezing outside and you want to get inside quicker)
- capturing star-trails (or other trails) or other HDR work (especially with moving clouds), basically where you're going to merge a lot of files together afterwards. If you're only taking one 30-second exposure every minute (where the other 30-seconds is being used to capture the dark-frame), then your star-trails may have gaps in the final picture.
It's different to the NR you get in DxO, DPP, Lightroom, etc. Long Exposure NR doesn't make your pictures softer like normal NR does. You can probably get the least noise when using both types of NR together.
YellowJersey - how do you enable the in-viewfinder level on the 5dmark3?