I use a few laminated weekly and monthly calendars on my wall (in addition to several Google Calendars), and the occasional spreadsheet for scheduling stuff, and for budgeting I almost exclusively use spreadsheets. Once you find a good template, or can create one, updating budget stuff is a breeze. Other than having someone else do it for me I haven't found a better way. Side note: I haven't personally used Quickbooks or a similar service, but I know a lot of people swear by those.
I realise everyone's needs are very different, but I've been happy with Freshbooks. It isn't specialised for movie making in any way, but I think it's nice to have a proper tool to manage everything from clients/contacts, receipts, cost of doing business and so on. It's also easy to generate professional looking estimates that split time based tasks from items that come with a fixed price. Once I had added my equipment and figured out my pricing for things like editing/grading, 2D animation, 3D animation and so on—creating an invoice is totally effortless and almost fun.
I also like that a solution like this allows me to send most things out digitally and it keeps track of if the client has seen the estimate and if it has been accepted. And there's an app of course, if you need to have a time tracker at the ready.
But like I said, this isn't so much about film budgeting per se, but more about finding a tool that works for you when running a (small in my case) business.
I think I might be answering another question here, and not what the OP meant, but maybe someone is looking for something like what I'm describing and gets a tip.