I do a simple work log on excel with time and dates that I work on the project and what I worked on, version of software, circuit board etc. I can't keep track of every aspect of a project. I have to review them if I work on them after not working on them for a while. I also keep a pin usage list in excel detailing which pin is used for what. The PC folder structure serves as my organizer. I also have printouts of things I consider important (say client sent in a description of diagram and I print and date) or convenient to have on paper, in a hanging folder. I don't know how formal you want to go. The more you organize, the more you waste time organizing :)
I also use a lot of boxes. I have boxes for each project, different size "Really useful boxes". I keep stuff I received for each job until the client asks them back. They usually don't, cause they keep coming back for updates and upgrades ;) .
So far it's kept my sanity and I didn't trip over too much stuff laying around. I also recently invested a bit on decent tools. Must have if you are ramping up your business. Can't be held back by cheap tools if others depend on your work.
This may work. I could keep a spreadsheet of active projects, that includes things like hours, delivery dates, costs, etc, and then just use the folder structure for storing files. I have taken a couple project management classes in college, so I am very familiar with the "The more you organize, the more you waste time organizing". Spend 4 hours filling out gantt charts, making reports, and doing calculations, all on 3 hours of work.
I also have the boxes of parts from clients. That was my first surprise. Customers spend all this money sending me this stuff, and none of them want it back.