What type of training/shape are you looking to get in to? My guess would be that you are looking to tone up - correct? That is usually the answer most people give unless there is a specific weight loss goal involved. With that goal, I would go for cardio first and weights second, but weights are great for getting into shape. Much better to do both than only one.
Why are squats out of the question? I know bad knees - got a couple myself - and with proper form squats really aren't that hard on the knees. Much easier than running! If you have talked to a doctor and they said this, then follow their advice. But don't discount it right off the bat.
I've heard mixed reviews of the Bowflex - but it is certainly more geared towards strenght training than cardio, and they are a bit pricey. If you have the option, head to a dedicated fitness store and check out what they have as nothing beats hands on experience. You might also want to look into Yoga or other low stress things like the Total Gym.
But the most important part of any exercise equipment is the user. They can all work, and they can all fail. Totally based on you.
