If my TFSA account is maxed and I want to transfer 5000 shares at $1.00 on August 2nd, 2011, and I was to sell the shares at $2.00 on January 3rd, 2012, would I have to pay tax on the gain plus 1% per month or only the 1% penalty?
First, if your stock is trading at $1 and you transfer the 5000 shares in-kind to your TFSA on August 2, 2011, you are deemed to have disbursed that stock in your (assumed) non-registered account. This may have tax consequences depending on the ACB of the original purchase.
As for your TFSA overcontribution, you will only have to pay the 1% monthly penalty on the value of the overcontribution, i.e. $5000. You will pay 1%/month for each month the overcontribution exists, regardless of what the value of the overcontributed assets end up being. Thus, you'll pay a $250 penalty for an overcontribution life of 5 months.
The stock price could go to $2 or $0, but you'll pay a fixed tax of $250 for the value of the initial overcontribution.