Some three-player online games are Tank Trouble, Multi Bomberman, Fish Eat Fish 3 Players and Big Birds Raching. You can find these games at either Y8.com or TwoPlayerGames.org.
Both Y8 and TwoPlayerGames have quite a few other options in addition to the previously mentioned games. At TwoPlayerGames, you can sort games by how popular they are, how highly they are rated or by the date they were made. At Y8, you cannot sort the games into different views, but you are shown games that are more played at the top of the page under the Awesome 3-4 Player Games section.