Include All means include all transactions with a transfer as the category. So if you pay your credit card from your bank account, it will be included in the report showing the category as [Credit Card].
Exclude All means ignore transfer transactions when preparing the report.
Exclude Internal is the most useful option. Suppose you are preparing a report which includes your Bank, Credit Card and Line of Credit account. This option means ignore transactions between these accounts. So when you pay your credit card bill, this transaction won't be included in the report. However, if you buy a car, and write a check to the dealer where the category is [My Auto], this will be reported, because it's a transfer outside of the accounts reported on.