Stained things are dirtied or marked in some way. You should probably reserve your stained pants for painting your bedroom instead of wearing them to a fancy restaurant.
Accidentally stained things are just dirty, usually permanently. Deliberately stained things, on the other hand, have a tint or dye applied to their surface: "I'm pretty proud of the stained walnut coffee table I made." An image or reputation can also be figuratively stained: "A stained reputation at work will make it harder to find a new job."