Hi,
After toying around with my Lego sets for a few months, I've kept them sorted by set (one big plastic bag per set). I will eventually assemble all the big sets over the next coming months, and this one-bag-per-set of course makes it easier to do. Every time I begin the assembly of a set, I sort all the pieces - I sort the big pieces such as wheels, bricks/beams, plates, and such on white tea towels on my dining table, and sort all the tiny bits (bushings, studs, axles, gears) in asssortment boxes - I found some nice transparent ones from "Lunar Box" on amazon.co.uk. I enjoy organizing and sorting, so I don't mind doing this for every build.
One thing I've noticed is that Lego from the 90's isn't quite the same as new Lego. For example, many of the old grey Technic pieces such as bushings and gears were blank / shiny, but most of the newly produced are matte. Old Lego also seems more "tight" to assemble, I think this is due to the ABS plastic becoming harder and ultimately more stiff and brittle. I can REALLY feel this with my old basic Lego from the late 80's - it's so hard and stiff to put together and even worse to pull apart. I do seem to recall that it was fairly stiff when I was a child/teen also, so I think they have "softened" Lego in the last decade or so, making it more flexible. Another issue is yellowing of old bricks. All in all, I think it would be a shame to mix 90's Lego with 2010's Lego, because some things will be mismatched, so I will continue sorting per-set.
I haven't dived into MOC yet, so that's another issue.