The Yamaha HP-3 was Yamaha's bottom of the line orthodynamic headphone in their original 1970s HP-x line up. The low-frequency response of HP-3/HP-50 headphones varies significantly from unit to unit and this is not yet attributable to any specific model variations. That is, the differences don't correlate with, say, cosmetic or packaging changes or, as yet, with serial numbers (see below).
Apart from the sound differences, it has also been noted that the HP-3 has been sold in at least two different retail boxes. Different packaging can be attributed to different production runs, or perhaps to different international markets for which the headphones were intended.
A notable difference between the HP-3 and the HP-50/a/s, is that the HP-3 often has a 'gasket' on the baffle side of the driver, whereas the HP-50 variants do not. HP-50a/s variations also have a white paper disc in front of the driver and leather imitation headband cover, whereas the HP-3/YH-3 sometimes do not.
It's possible that the sound differences in HP-3/50 models can be related to their serial numbers (stamped inside the left side of the headband). Here is a provisional list of serial numbers with comments:
HP-50S: 162906 - used to belong to DAC
HP-3: 270880 - Tony's HP-3 - Bassiest pair known (still underdamped after usual damping for bassy pairs), from UK
HP-3: 390282 - Ludo's original HP-3 - Bass-heavy with super-loose diaphragm
HP-50S: 463014 - Kabeer's HP-50S - Bassy HP-50 from France
HP-3: 770738 - Ludo's office HP-3 - Bass-heavy sound but less damping required
HP-3: 771138 - The “Irish” HP-3 - Bass-light HP-3
HP-3: 781739 - World Tour HP-3 - Tensioned diaphragm, almost no damping required, not a lot of bass. From Germany
HP-3: 830446 - Kabeer's HP-3 - Bass-heavy from USA
HP-50A: 920115 - Kabeer's HP-50A - Bassy HP-50 from Germany
HP-50A: 1y1133 - Shivesh' HP-50A - Bass-heavy sound but less damping required from Lincolnshire, United Kingdom