This is a good question that comes up constantly. There are a lot of possible methods, but one of the most important things is to recalculate every couple of years and make sure that how you're currently organizing still makes sense to you. It depends a lot on how much space you have, how you're trying to organize, your collection goals, etc.
When i started i stored all my cards in booster boxes. Then i got some 1k card BCW boxes. I've been using 5k card (5-row) BCW boxes for about 20 years now. They're the densest storage method I'm currently aware of, which increasingly matters as your collection grows. I'm lucky to have the right space for the 5-row boxes which would otherwise be a little unwieldy/bulky, and they've survived multiple moves in that time.
In regards to WotC's recent printing policies... not only are they starting to print a million variants, but they're also RE-printing a lot more than they used to. A definite advantage to cataloguing your collection is to make sure you're also not keeping too many of any one card. I'd suggest not keeping more than one playset of any particular edition of a non-reserve-list card. You can use the Card Database which will list how many of each card you have in the left-hand column.
Good luck!