Gavin Andresen - 2011-03-09 19:18:53

1) bitcoind - I think this might be the same as configuring bitcoin to run as server. I believe it uses an RPC API to run transactions from the command line.
Pros: Everything stays on my server
Cons: I have to find a server that will let me compile and install this, rather than just some PHP/MySQL farm in the cloud, which is what I prefer

You can run the front-end on one server and the back-end on another (and communicate via JSON-RPC over HTTPS).  That's how I'm able to run the Faucet and ClearCoin on Google's App Engine (they talk with bitcoind processes running on linode.com and aws.amazon.com servers).  bitcoind doesn't take much memory, bandwidth, or CPU (just don't turn on coin generation), so, for now, anyway, you can even use an Amazon "micro" server (which costs something like $100 per year).

I'm not selling anything so can't comment on the shopping cart interfaces.  Screen-scraping web pages is a bad idea for lots of reasons.