I too used to lose a lot of loose sheets of paper. I follow the discipline of writing everything into a spiral bound notebooks. I have tried using SimpleMind (runs on both iPad and MBP), but after a while I realised that so much synergy arises from flipping through the pages of notebooks. Only once I have a reasonably clear path for implementing an idea, that I start documenting the design in a collection of computer files. Even then I often print stuff out and file them in a ring binder, along with the original notebook pages.

No matter what I have tried over the years, no application has the immediacy of flipping through paper pages.

With an iPad (soon to be universal) app that I primarily built for myself called Mindscope. It's basically Workflowy meets Scapple - visual and simple like Scapple, but you can drill down into sub-groups like Workflowy to not get lost in details. http://www.mindscopeapp.com