I started with SPDs, and they were fine for a long time. At first I had some knee pain, but after a fitting to make sure the cleats were positioned right on my shoes they were okay and I had no complaints for several years.

However eventually the knee problems came back, and then when I got a new bike they were worse, so on the advice of the fitter at the LBS I switched to Speedplays (not sure of the specific model -- X-somethings). They have more float and my knees are much better with them.

The only downside I find with the Speedplays is that it's very hard to clip in and out if dirt gets in the cleats. I bought some cleat covers (plastic covers that snap on) and bring them with me whenever I ride so I can use them if I need to walk anywhere. It's a bit inconvenient, but better than painful knees.