If you are using active glasses, ambient light can contribute to seeing a little bit of flicker and might contribute to viewing fatigue. Also, all 3D glasses darken the picture, and ambient light competes with the picture on the screen, making it look even more dim. So, it is usually best to watch 3D in a darkened room.
I watch 3D content on my computer monitor, and it's slightly reflective. Given that the reflection is at a different focal distance than the images on-screen, it throws me off a little, so I prefer to watch long videos (i.e. movies and not just 2-minute YouTube vids) in the dark.