I absolutely LOVE http://www.freshbooks.com
Cloud based accounting and they’re adding features almost monthly. Its really straight forward with a clean, simple interface. Ability to generate a number of reports including P&L, expenses, invoices by client, status, etc. and they just added a feature to allow connection to your banks account for automatic expense tracking.
One thing I do though is I like to generate my own invoices via excel. I just prefer my template. I track time and expenses via fb and generate the invoice I send out via excel. When I send I mark the inv as ‘sent’ in fb and paid’ when its paid, etc. Works flawlessly for me. I have the $19.95/month plan.