Agree with both of the above posts. Pay close attention to your favorite company's home-grown points program (e.g., Hertz #1 Awards, National's revamped Emerald program, etc.) as well as the opportunities to earn hotel points for your rentals. Based on your own personal value and need for car rental or hotel points, you can make the best decision for each rental.

Hotel points are typically a fixed amount - perfect for short, cheap rentals. The rental points (at least at Hertz and Budget) are awarded per-dollar, making them perfect for longer or more expensive rentals. The breakeven point varies based on your own valuations, but for me it's about a $70 rental (More expensive, and I opt for Hertz ZE1 points. Cheaper, I take Marriott points.)