i built corduroy (http://corduroysite.com/) after getting fed up with trying to use quickbooks for my small business, and most other web-based apps at the time were just project management or invoice creation.

i use my business debit/credit card for almost everything, and send checks out for my monthly bills. with corduroy i can receive a bill, print a check for it, and then automatically download the transactions from my bank to mark that check cleared, and quickly categorize all of the new debit card transactions. at tax time, i just go through each of the categories and put the totals into the tax software.

of course it does invoicing and project management, too.