Hey, I don't know about 16x16, but many many roguelikes allow modding.
Some I've modded myself include Brogue (there's a build where Oryx added tiles, and you can use that build and mod Oryx's tiles), Slimey Lich Mummy (PNG file if I remember right) and Infra Arcana.
Most are going to allow modding. Tome4 I'm pretty sure does, Crawl does most certainly, so does Nethack. Most all open source games have a simple bitmap or PNG file you can fiddle with.
I had the most fun modding Slimey and Infra. Infra because it's just a fun game period, and Slimey because the tile resolution looks great on screen. It's tough to find one that produces pixels on a 4 to 1 ration when displaying on screen. Pixel art, to me, looks best when it's AT LEAST blown up double, so 1 pixel becomes a 2x2 block.
Also Slimey is about the size you are looking for, 20x20 I think.
I've never done an entire set but I've had a lot of fun with what I've been able to do.
Here's a link to me yammering on even more about it and some pics of what I did:
http://forums.roguetemple.com/index.php?topic=2934.0