http://freeagentcentral.com is the best web based accounting system there is. I've used Freshbooks and Blinksale before but these guys handle almost all accounting needs end to end for a small business. Although primarily UK based they have a universal version that works world wide.

They also have a beautiful API so we can fill in any gaps very easily ourselves and they're adding new features every week... and they are probably one of the top users of http://getsatisfaction.com.