When I calculate "interest" rate on my Stock Investments, do I include commission fees?

If commissions take up 20% of your overall profit, perhaps you need to find a different broker. Online brokerage houses cost $4-$12 per trade, so you are either making a Lot of trades or trades involving very little money.
Compound interest is not what you do to value a stock portfolio, rather it is capital gains/losses.
And commissions can be somewhat deductible.

It really depends on what you're calculating your interest rate for. If you just want to look at how successful your bets have been, then I would exclude commissions. If you want to take a broader look, and you're just interested in how much value you have generated for yourself, then definitely, include those commissions.
You started talking about overtime at work, which doesn't really seem to relate to your question. Perhaps if you could give some more context we could give a clearer answer.