Well for the in-dash, I would just get something you like and are comfortable with. I have an Eclipse unit myself, its awesome. But I really like the Pioneers a lot, some of their less expensive models are still packed with features and have great screens and function.
Speakers, well I guess it depends on what your preferences run to. I have always been a fan of Infinity components. Great sounding speakers with great clarity and sound quality. There are others just as good or better, but for features and price I have always been an Infinity fan.
As far as a sub and box etc, I give my regards to the hotbox. I think one of our sponsors makes a version of this as well. It will take up your center seat portion and is a great enclosure. The sound is phenomenal and the price isn't too bad either. I have an Audiobahn alum10Q in mine and it hits great, but everyone tells me this box was practically built to be a perfect match for a JL Audio 10w3 I believe. Best of luck in getting what ya want.