We just completed a major home renovation, and for slab, we found Amazon Stone on Miramar Rd generally has best selection and price. Also check Tutto Marmo off Miramar Rd (I think they’re on Cabot, but I’m not sure). They have beautiful slabs, and some unique stone/limestone/onyx.
For subway/mosaic tile, it depends on what you’re looking for…if you want standard 3×6 subway, there’s no need to spend much money. You can find lowest prices at Dal Tile, Home Depot and online. Check out http://www.costco.com as well for standard mosaic and subway.
If you’re looking for tile that’s a little more unique, the local sources I like best are: Euro Tile Art off Morena Blvd, Unique Stone Imports on Morena Blvd (they also have a stoneyard for with interesting slabs), and in No. County, you should check out Encinitas Tile.
I also went up to the Walker Zanger tile showroom in Tustin, where I found great ideas from wandering through their gorgeous displays and beautiful tile. They also have a large slabyard filled with high quality stone, and, surprisingly, the prices aren’t generally any higher than around here although your fabricator would have to go there to get it. W-Z expects you to be working with a designer, but if not, you can tell them you want contractor pricing (if your contractor allows you to take advantage of his discount). You should make an appointment if you decide to go there.