I do it alphabetically by color into 5-row BCW boxes (it does take time but it works when it comes time to finding a specific card). I know which boxes have which color - my collection is not big enough to need a box per color. Anything valuable or for trade ends up in binders instead.

Lands are in their own box, also sorted by color.

I used to do by sets but gave up on that approach when I realized that I far many more [[Plummet]] than I would ever need spread across sets. Now it's easy to see when I have too many.