Depends on which 3 day rule you're referring to, so I'll give examples from TD Ameritrade, as that's what I use.
Depositing funds via electronic transfer from your bank account. Funds are available for use the same business day for Big Board stocks, however, those funds cannot be used to buy OTC stocks for 3 business days. For example, I deposited funds from my bank before the market opened on Thursday. When the market opened, I was immediately able to buy Big Board stocks. However, I had to wait until Tuesday until I could buy OTC stocks.
There's also a 3 day rule for buying/selling... funds take 3 business days to settle.
Example 1: You buy $1000 of Stock A on Monday, and flip it for a quick profit on Tuesday. You sold for $1100. That $1100 will show in your account balance, but it will not be available for trades until Thursday (3 business days from the original buy).
Example 2: You buy $1000 of stock A on Monday. You hold it and sell for a profit on Thursday. Say that, again, you sold it for $1100. That money is immediately available, as 3 business days have passed since the original buy.
Other brokers have different limitations, i.e. I remember someone posting recently that said ETrade has a 6 day wait for electronic bank transfers.