If we limit the discussion to just the method claims (because let's face it, the invention will be in the method for e-commerce applications)
Ah, but you should not limit the discussion. There are important differences between method claims and system/apparatus claims. Some of which were already discussed by MYK, and related ones which I address below.
Should we be sure to state that everything is being done and received by a server, such as in this application:
What's your thinking here? ie, explain what you think the consequences are for including the term "server", and for not including the term.
Does Bilski change things for how e-commerce patent claims should be drafted?
Ah, that's the million dollar question. Seriously. No one knows yet. The Fed Cir has not yet decided a post-Bilski case involving what I would call an "e-commerce" patent. RCT v. Microsoft looked at a method claim for processing images, and found it not abstract. That's the only Fed Cir guidance that we have so far.
See the RIMM v NTP case for what happens when you only have method claims. You *need* that valid system claim, otherwise if any single step is performed outside the USA, there is no infringement.
Centillion v. Qwest points out another advantage of system claims over method. Namely, if the system claim includes client elements and server elements, the entity operating the client may be found to *use* the system as a whole. You can then go after the entity that operates the server for indirect infringement. Without the Centillion holding, there can be no single direct infringer of such a claim, and thus no indirect infringement. That leaves only vicarious liability, which simply doesn't exist in many fact situations (see, e.g., Golden Hour Data System v. emsCharts and Akamai v. Limelight).
The better approach is to avoid claims that look like those in Centillion, Akamai and GoldenHour. That is, don't write a claim which includes the actions of, or components operated by, two different entities. But sometimes that's easier said than done, so it's nice to have Centillion to fall back on.