The 3 cam positions is fairly common accross the toyota range. The 3S series of motor has them as well.
In a nut shell, it is to fine tune the alignment of the cams. As they don't always line up because of a few factors (like the belt being slightly off etc..)
The pins can also be used to retard/advance the cams if you so wish.
http://ugbox.net/~lance/GT4/Technica...ing%20belt.pdf <--- this document is specific to the 3sgte, but is the same idea. On page 12, at the top, it talks about lining up the cam wheel and then inserting the pin in th eappropriate hole.
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