I don't actually think Barack Obama's remarkable advantage in small-donor fundraising is all that inexplicable. As a Dean Campaign alumni, I'm contractually required to believe that raising tens of millions from small donors is an internet-based phenomenon. And, largely, I do believe that! The techniques pioneered by MoveOn, the Dean Campaign, and others of their ilk are enormously effective at getting engaged citizens to donate small amounts of money. And if your e-mail list is big enough, that translates into huge total sums. So, when comparing Clinton and Obama's success, it's worth looking at their web traffic -- if Obama's got more folks coming by the web site, he's going to have more folks to ply those techniques on. The following graph is from Alexa, which, though inexact, is about the best traffic comparison tool we have:
Obama's site gets way more traffic than Clinton's (and both get way more traffic than McCain's -- he's that little mustard colored line near the base of the graph). And with way more web traffic comes a way larger e-mail list, and with a way larger e-mail list comes more donors who eventually succumb to a fundraising appeal and donate $20, and when they do that, it becomes far more likely that they'll do it again, as now they're invested in the campaign. Add in that a pretty high percentage of Obama's voters are fervent backers, rather than soft supporters, and you have a recipe for some impressive fundraising.
Obama's site gets way more traffic than Clinton's (and both get way more traffic than McCain's -- he's that little mustard colored line near the base of the graph). And with way more web traffic comes a way larger e-mail list, and with a way larger e-mail list comes more donors who eventually succumb to a fundraising appeal and donate $20, and when they do that, it becomes far more likely that they'll do it again, as now they're invested in the campaign. Add in that a pretty high percentage of Obama's voters are fervent backers, rather than soft supporters, and you have a recipe for some impressive fundraising. 
