MT raises a good point about rep ranges and loads. Cycling the frequency with which you train heavy, should help.
Also, as Chad Waterbury has mentioned frequently, it is important to exercise through different planes of motion as training one exercise (and thus one movement pattern) too much can lead to overuse injuries.
Thus variation in movement patterns will, arguably, assist in keeping you injury free. If, for example, you wanted to perform energy systems training multiple times per week, you might consider running stairs on on day, treadmill on the other, rope skipping on another etc. These exercises aren't just different - they involve different movement patterns and, thus, load the target muscles differently (and, moreover, subject the target joints to stress in different degrees and from different angles).
All of which is good for joint longevity. Training in this way provides the benefit of frequent training of a particular capacity (in this case energy systems work) without over-training any one given movement pattern.
As I've been told before (and discovered after much trial, error and pain), change is like rest.
Finally, if you're not already taking a good quality omega 3 supplement, you may wish to start. Omega 3's are useful for their anti-inflammatory properties (bear in mind, however, that an omega 3 supplement will probably take several weeks to fully saturate at the cellular level, so stick with it).
Also (I know I said that my point above was the last one, but the coffee's kicked in and I really couldn't resist!), pain in a joint can often be caused by tightness in the surrounding muscles. As you're probably already aware, when a muscle tightens it shortens, pulling all the associated structures out of neutral alignment (to varying degrees, depending upon the severity of the tightness). Thus, you may also wish to investigate and seek to stretch any tightness in the quads, hip flexors, muscles of the lumbar spine, etc.).