As a general rule I prefer direct deposit because, as has been mentioned, I am not providing information beyond that which is on the face of my checks. My understanding is that a direct deposit can be reversed, but it is extremely difficult to do judging by my attempts to get someone else's direct deposit reversed back to sender when it erroneously landed in my bank account.
I gather that Paypal is easier to reverse out, though still not simple. I transfer Paypal payments on to a savings account at the same bank where I have checking and transfer the money on along to my checking when the payment comes in, leaving only enough in the savings account to keep the account open. This means that if there is going to be a reversal I need to be involved in it because if there is not enough money in the account, Paypal is not authorized to create a negative balance in the account.
Paper checks, which would seem to be the safest form of payment, are actually the worst because they can be written on an insufficiently funded account and bounce, they can be delayed or lost in the mail and before remote deposit, could even be forgotten on my desk for a while.