High profile is a more generic preset. It activates a number of options that allow for better compression. The ATV2 setting is obviously made to push out an encoded file that will utilize options optimized for ATV2. If you are unsure of what you are doing, it is a good idea to use the preset.
The ATV2 setting is sure to produce a file that can playback on the ATV2. I have not tried it but it probably reduces frame size to 720p (ATV2 will accept 1080 but it will downsample it to 720). Again, I don't use the ATV2 preset because I like to tweak settings anyways. If you don't know what you are doing, it is best to use the ATV2 setting. The additional benefit of doing so is that the resulting files can also playback on current generation apple mobile hardware.