I took my engine apart and one of the things I noticed, on both cylinder heads of my Tacoma V6, is that the intake valves (picture right) are significantly darker (or dirtier) than the exhaust ones (picture left). Why is that the case?
Exhaust valves are hotter because they are venting the combusted hot air. This causes them to not collect deposits or burn of any thing that tries to deposit on them. Intake valves are constantly receiving a cold charge of air/gas coming in. They run cooler and deposits tend to collect on them and you'll get a nice dark carbon layer on the bottom. If you look at the top side of the intake valve it will likely have buildup as well due to this.
The main reason the intake valves show more carbon buildup is because in most fuel injected engines (newer direct injected engines excluded), the fuel injector fires right at the back of the intake valve. This means some of the fuel gets stuck on there and you get a build up of it over time.
As @elmerfud said about the exhaust valves is spot on. They are cleaner because they are baked clean from the heat.
As an aside, since direct injected engines pushes fuel directly into the cylinders, there isn't any fuel to collect on the back of the valve. Some of the manufacturers are seeing issues with this because the valve is too dry. This can cause wear which wasn't there when the fuel was present.