Tinker with the handlebars and saddle. The problem with knees is that they move repetitively through the same range of movement when you're on a bike, so changing the height of the saddle now and then will put them through a slightly different part of the range. Also watch what your feet are doing - if they're turned outwards, or if you're twisting your foot slightly as you pedal, that will also cause strain on your knees. Changing the height of the handlebars will alter the amount of weight taken on your wrists - the lower they are, the more weight falls onto them. You might also want to try the sort of handlebars that have a forearm rest and change from drop-type to straight or vice versa - in short, experiment first before you give up.