Google Checkout was very good with their fraud protection to the point that I did not have to think about it. In fact, over the years I have been growing my business Google have been my rock---never a real issue with them.
PayPal was a similar story but it also seemed to attract the sort of customer that would open a dispute at almost any issue (or just threaten it). You can also count me in one of their horror stories that indirectly cost me £5k and even got to the point where they just flat out refused refunds for my customers who wanted them.
I have a Stripe and GoCardless account as well and I've been trying to make it work but their fraud protection is just not up to scratch compared to Google and PayPal, which is a real shame. I'm not sure if I'll ever be able to see enough data to get quite the same fraud protection. Stripe do look fun though.
Another perspective from a merchant: roll on Bitcoin. With exchanges offering guaranteed payouts in another currency (for me, GBP) I take on zero risk by accepting it and it solves so many problems. There's no wonder more and more websites are starting to accept it.