I just discovered Autechre, and I am kicking myself for not listening to them earlier. Also, I've only listened to one of their songs so far, but I love it. "Second Bad Vilbel" from 1995's "Anvil Vapre".

Somewhat less-known compared to most artists named in this thread, but I've liked Somatic Responses for awhile. They're kind of IDM-ish, sometimes more rhythmic noise. Their tracks are really complex and intricate, sometimes interrupted with slow beautiful moments of piercing chords. I'd especially recommend their double album "Adverts" from 2003.

As for Aphex Twin himself, most of his music tends to bore me. I mentioned Autechre to a friend the other day, and he said, "They're like Aphex Twin but not boring?", and I pretty much had to agree with that. (from what little Autechre I've heard, mind you)