Ive done a good number of payment systems for websites, the important thing to consider is "who deals with the credit cards?" (aka, where are the payments actually made)

If you choose to take payments ON your website, you will need a cart system and a payment processor. You will also need security (SSL cert).

Most typically prefer to let someone else deal with all that by using something like 1shoppingcart or many of the other integrated cart systems out there. Paypal is also very convenient in that they do it all.

Generally, if you will be handling a lot of transactions and moving a lot of products, you will retain the largest profits by handling everything yourself (youll still pay some transaction fees). If initially you only expect to sell a few products here and there, definitely look into Paypal since its one of the least complex systems out there (it also scales as your business grows).

Hope that helps!