Laying a tower case on its side for maintenance, such as installing the motherboard or a video card, is normal, and you want the computer off first for that. Make sure any optical media is removed first. Powering it on while it's still horizontal is risky, unless (as iceclock mentioned) your case is designed to be horizontal.
Do a google search you will see it's not a big deal provided you arn't hurting the airflow to much and heat is still able to be easily pushed out. Obviously make sure you mobo is facing up and not down like I said before. And like I said before the optical drive may or may not end up having issues.
Also I would not advice sitting anything on top of it as the side panel isn't made to take weight like a top panel might me for a horizontal case.