I also use RescueTime and OmniFocus. There are plenty of paid apps on my phone / tablet / computer, but those are ones that I would struggle to replace.
The paid app I would love to get rid of: Quickbooks.
I run a business without Accounts Receivable and just need a reliable way to keep books. However, it is not a simple business. We have multiple revenue centers (departments or classes), multiple bank accounts, and multiple cash accounts. Intuit seems to be moving away from companies like mine (oh, and I use a Mac).
I was really excited when they moved Quickbooks Online to a more modern interface. Unfortunately they made some frequent tasks (browsing our chart of accounts) much more difficult that it used to be. Invoicing is much more prominent though.
It has its flaws, but it's made a big difference as a catch-all brain bin for me.