Some suggestions.
- Scapple: it‘s very flexible with both notes and images; however, it won‘t end up in nice tabular structures
- Gimp: at least want to mention it
- Office tools, both Microsoft or OpenOffice: spreadsheet, presentation; consider using databases
- Tikz and Latex: tikz provides nodes, which can include graphics, can be positioned free, bound, on a lattice etc.; Latex provide the host document for tikz, e.g. with
\documentclass{standalone}