I'll share what I think would be a good system, that unfortunately I never used myself, so I am semi-disorganized.
I think the ideal system would be to create a simple database (use Access or whatever other free db out there). In the DB, you can fill in fields for all the details, like type, brand, purchase price, from whom you bought, test readings, whatever else. I think you should also have a field where you have some code that identifies pairs/quads. All of these would be easily searchable because DB's let you sort and search by fields. But here is the cool thing; databases are designed around a key that identifies unique entries. Write this key on the tube box, so that you can look up the key for a tube and bring up all the details you entered.
For storage, I have a large craftman's tool case and surprisingly the sizes of the different drawers fit the different size tubes I have quite well (I have hundreds). I have them organized by type and where possibly many of the details are written on the boxes, but the price paid and other notes would have been nice to have kept track of.
Also, for me it would have been nice to know what design usage inspired the purchase as I don't typically buy the usual suspects (12A*7, 6DJ8, etc).
You can very quickly build a form in access or similar that you use to input all the fields, which makes it simpler. Or if you don't want to bother with a DB (although there is advantages to doing so) you could always just use a spreadsheet, although I highly recommend creating a "key" for each tube to be written on the box.
