Randy Smith, of Looking Glass’ Thief, has a GDC 2009 talk: "Helping Your Players Feel Smart: Puzzles As User Interface".
Jonathan Blow has an older talk that brushes the topic a bit: "Indie Prototyping, Braid, & Making Innovative Games".
Google the text in quotes; I can’t link URLs.
I remember Alexey Pajitnov presented another great deck somewhere about designing Hexic, but I must have deleted and have no reference for it.
Find anything yourself, post it here.