I use Microsoft OneNote.
I collect all the data in excel so I can manipulate it as needed.
If your using a LabView program you can attach the Vi’s.
I will take photos with my camera.
I’ll save Oscilloscope, Network Analyzer, Spectrum Analyzer, etc. screen shots.
I put all this in OneNote. You can add the manufactures data sheets, web links, and whatever.
You end up with a story book of your project.