Separate your commons and uncommons into one pile and your rares and mythics into another pile. (When pricing collections, I use $0.75 as my threshold, since they're the ones likely to pop over $1.00 on occasion.) Go to a website of your choosing that lists the prices by set, and filter by the price so you only see prices over a certain threshold. Once you have them sorted by set, you'll want to go through each set and find the value cards. There's a very nice guide to identifying sets on this site. I sorted a collection of 10,000 cards in five passes, but I used my knowledge of the block structure to help with that.

If you find there's too many sets, then only pick out a couple of sets per pass (ideally the ones that have the most, to reduce the amount of picking on the next pass). Remember that cards will naturally have some order to them, so you will likely have a lot of runs in the same pile.

I suggest you do this with the cards upside down if you're right handed so it's easier to thumb through them. This will make them much easier to look up. The first thing you'll want to do is sort the cards by set. Bulk cards are usually valued by the inch (for example, they'll buy for $0.20 an inch, which works out to about $0.005 per card) so getting value cards out of the bulk pile is paramount in properly valuing a collection. Your first goal is to separate bulk from value.

Mtg card sets by year value