Altcoins: Determine how many confirmations to require to deposit For Bitcoin it is common knowledge that 6 confirmations suffices. For the hundred of Alt Coins however, I'm not sure what the best practise to be protected enough from double-spents and the likes is.

I saw Bter.com requires different confirmations varying on which Altcoin you want to deposit.

For example COMM-coin requires 10 confirmations, but BBQ coin 6, and Infinitecoin only 4.

Is there a mathematical method behind this? How do they know how many confirmations to require?
Yes, there is a mathematical grounding behind this, namely Poisson distribution. See Satoshi's original paper (last pages) for some details about calculating the odds of a successful double spend attack given a certain portion of the networks computation capacity. This also means of course that networks with a larger hashing power are more susceptible to an attack than networks with lower hashing power.