I had a cheque for my taxes stolen on its way to the Inland Revenue a year or so ago, which caused quite a bit of trouble, though as it happens the Revenue and my bank were *very* good about the whole thing.
So reluctantly I'm using cheques a little less and for significant sums paying over the phone instead (and watching the balance drop in my on-line bank account in real time). I think that the on-line credit card security systems are crap, though they are now a little better when I last had anything to do with them for work as CTO of an on-line credit-card firm, and I avoid on-line payments whenever I can.
I see doing more direct bank transfers in the future, on-line, as cutting out a lot of trouble in many cases.
Rgds
Damon
PS. PayPal! Because BoA wrongly shut my personal checking US$ account, PayPal has frozen my account with them ever since, and I've been unable to unfreeze it.