Without clicking any check boxes on MT Gox I have got my bitcoin very fast (maybe 10 minutes). After 3h I have got 17 confirmations. Is that good? For my next test I have checked the "green address" option. Again I have sent a bitcoin to my address. Got 12 confirmations untill now. The third bitcoin I have transferred with the 6 transaction check box on. It has 13 confirmations untill now. Do I really control this coins now?
0 confirmations: You control the coins, but a good attacker could still "double-spend" the coins elsewhere, causing them to no longer be yours by making the transaction no longer exist. If the transaction is coming from someone you trust, though, you have nothing to worry about.
1 confirmation: The transaction has been added to a block and the only way that the transaction can be undone at this point is if another block conflicts and overwrites this block. This happens fairly often just by random chance, so if the funds came from someone you don't trust, you should still wait.
6 confirmations: The network completely agrees that this transaction happened, and the transaction is almost impossible to reverse. Even if it is reversed by a strong attacker, the effect of such an attack would cause the development team to release an updated version of bitcoin that will lock in this original branch of the blockchain.
When it comes to how quickly you can be certain you own the bitcoins, what matters is how long it takes to receive the first confirmation. After that, every block that ever gets released "confirms" your transaction automatically.