Merchants who *really* rely on their web site being secure are those that take instructions for the delivery of value over them. It's a given that they have to work very hard to secure their websites, and it is instructive to watch their efforts.
The cutting edge in making web sites secure is occuring in gold community and presumably the PayPal community (I don't really follow the latter). AFAIK, this has been the case since the late 90's, before that, some of the European banks were doing heavy duty stuff with expensive tokens.
e-gold have a sort of graphical number that displays and has to be entered in by hand . This works against bots, but of course, the bot writers have conquered it somehow. e-gold are of course the recurrent victim of the spoofers, and it is not clear why they have not taken more serious steps to protect themselves against attacks on their system.
eBullion sell an expensive hardware token that I have heard stops attacks cold, but suffers from poor take up because of its cost .
Goldmoney relies on client certs, which also seems to be poor in takeup. Probably more to do with the clumsiness of them, due to the early uncertain support in the browser and in the protocol. Also, goldmoney has structured themselves to be an unattractive target for attackers, using governance and marketing techniques, so I expect them to be the last to experience real tests of their security.
Another small player called Pecunix allows you to integrate your PGP key into your account, and confirm your nymity using PGP signatures. At least one other player had decided to try smart cards.
Now a company called NetPay.TV - I have no idea about them, really - have started a service that sends out a 6 digit pin over the SMS messaging features of the GSM network for the user to type in to the website .
It's highly innovative and great security to use a completely different network to communicate with the user and confirm their nymity. On the face of it, it would seem to pretty much knock a hole into the incessant, boring and mind-bogglingly simple attacks against the recommended SSL web site approach.
What remains to be seen is if users are prepared to pay 15c each time for the SMS message. In Europe, SMS messaging is the rage, so there won't be much of a problem there, I suspect.
What's interesing here is that we are seeing the market for security evolve and bypass the rather
broken model that was invented by Netscape back in '94 or so. In the absence of structured, institutional, or mandated approaches, we now have half a dozen distinct approaches to web site application security .
As each of the programmes are voluntary, we have a fair and honest market test of the security results .
 here's one if it can be seen:
Hopefully that doesn't let you into my account! It's curious, if you change the numbers in the above URL, you get a similar drawing, but it is wrong...
 All companies are .com, unless otherwise noted.
 As well as the activity on the gold side, there are the adventures of PayPal with its pairs of tiny payments made to users' conventional bank accounts.
 I just thought of an attack against NetPay.TV, but I'll keep quiet so as not to enjoy anyone else's