I look at a company like Remember The Milk and wonder how much they could possibly afford to pay. A quick back of the envelope calculation based on compete.com, 170k visitors/month. Let's say that 80k are customers and 8k are paying customers ($25/year), and that their yearly revenue is $200k. They have three or four full time people and increasing traffic.
I guess a company like that could afford to pay $10-20k/annual for a license. That might even be considered a good business decision given that with their current revenue they probably don't have a lot of money in the bank to fight a legal battle now, but that with their growth they have future profits that should make this a minor annoyance.
If you and/or the other defendants don't litigate the validity of the patent well and lose that issue, future parties are barred from re-litigating that issue.
A strategy of a small guy is to try and bring in a large guy to litigate an issue that will be very important to them in the future (i.e. eBay, Amazon, or whoever else may be infringing the patent).