I'm frankly pretty terrible at this, but I'll try to help a bit.
For resistors, I organize them by value range, so...
100r, 1k, 10k, 100k, 1m all together, 47r, 470r, 4k7, 47k, 470k, all together, etc. Probably an easy way to get mixed up with parts a full decade or more off spec, but I've not had problems yet. Transistors sorta go by type and series, with my drawers in one parts organizer being labeled:
| BC108 | MISC NPN | J201 | 2N5457 | J113 |
| MPSA18 | PN2907 | BC549 | BC550 | |
| 2N3904 | 2N3906 | PN2222 | | |
| NOS/VOS PNP | NOS/VOS NPN | 2N5087 | 2N5088 | 2N5089 |
I'm interested to see what others have to say, bc I have a ton of drawers. that are labeled misc 1, misc 2, etc, and they're just complete nonsense