Basicly light can get in the viewfinder in long exposers in some case and screw things up.
Don't live me credit for this copied it of some other forums
The problem is the exposure meter. The sensors for the meter are located in the prism area, and of course they measure whatever light hits them. They cannot distinguish between light arriving from below (ie through the lens) and light arriving from above (ie through the viewfinder).
This can be quite significant in some cases. If you're shooting with the sun at your back, you could pretty much have the sun shining directly on the meter, causing the picture to be drastically underexposed. Of course, if you are looking through the finder when the reading is taken, you're blocking most of that, so it's normally no big deal. But if you're using the self timer, a cable release or a remote trigger, you aren't there to block that light.
Using the eyecap is not necessary - anything that blocks the light is sufficient. Your hand, a dark t-shirt, etc all work.