I was looking at the Omega 960gs theme, and came across the assertion that using it would preclude any need for using panels. After looking deeper into what the theme does, I'm fairly confident that while there is overlap, the theme doesn't do offer everything panels does. Not that it should...it -is- a theme.
I'm starting the conceptual design of a site that will be D7, with OG and Drupal Commerce and many other distinct sections, so a strong need for intelligent contextual layouts. I made a first-pass module list (stopped counting at 100), and of course it began with panels. The reading I did about Omega raised an abstract question... what considerations should there be when selecting a theme to use in conjunction with a site controlled by panels and panels everywhere in terms of what would make a theme work best with them, and what advanced layout capabilities (grid? dynamic regions?) would still be useful, and which would cause problems?
If there's a D7 theme that's minimal and clean that would behave better with panels than others...