If you're new to the sport and wondering if you need to stretch on a regular basis, allow me to enlighten you.
I know some elite athletes who advocate a no-stretching training plan. I've heard about studies that reveal that top runners have compromised flexibility in some areas. So when you win Ironman Wisconsin (after completing Ironman Louisville the previous weekend) or can call yourself a "top runner," you may discontinue stretching.
Until then, this is very, very important.
The tough part is knowing what stretches to do. Besides the stretches you learned in grammar school gym class, that is. Here are some areas of particular concern to most of us swim/bike/run specialists.
Backs of the legs. There are three hamstrings--one that's more towards the outside of your leg, two more towards the inside, so try to work in stretches at multiple angles.
The IT band isn't actually a muscle; it's a long band of fascia that connects the tensor fascia latae to the knee. It gets really tight in runners and cyclists, so what does that tell you about how it must be in triathletes? It's hard to stretch, so you may also consider rolling it out on a foam roller.
This one will get particularly bad if you spend a lot of time seated (i.e. at a desk, driving). Tight hip flexors can throw off your whole posture. They'll make kicking in the pool more difficult, and can contribute to the problem of overstriding when you run.
Deep Hip Rotators/Glutes
These muscles (the piriformis, in particular) took me out for 4 weeks last season, giving me only 2 weeks to prepare for my first race of the year (took me out again in the fall, spoiling my marathon training). Tight hip rotators and glutes can cause low back pain; a tight piriformis can lead to sciatic pain.
Tight calves are very common among triathletes. This can cause a problem when you get off the bike (which uses quite a bit of calf engagement, if you're doing it right) and start running. Tight calves can also aggravate your achilles tendon. To stretch the gastrocnemius, perform a calf stretch with the knee straight; to get more into your soleus, bend the knee slightly.
Most Americans are very overdeveloped in the anterior muscles, again because we spend so much time sitting and hunched forward. This problem is exacerbated in triathletes because we primarily swim freestyle. It's extra important for us to stretch these out, though, because it improves our posture (particularly crucial for running) and prevents overuse injuries.
Ever get tightness or pain in between your shoulder blades? It's probably these muscles.
Spinal extension muscles. I've got a "Stop Slouching" article coming soon that specifically addresses these. Triathletes have a fairly unique problem, because we have to shorten these muscles to look up and forward when cycling. There's really no way around that, so it's vital that we stretch these muscles on a regular basis.
Those are the basic stretches that I would recommend. Alternatively, you could join a good yoga class that emphasizes flexibility (if you're trying anything with the words Vinyasa or Power in the title, you're probably barking up the wrong tree). I advise stretching for around 20 minutes a day, but I know that's not gonna happen for most of you. Let's just say pick 2-3 stretches to do after each workout, planning to get through all of them every couple days. If you'd like a second opinion you can check out this guy's stretching routine.
Just try it for a while. You can always give it up, if you want, once you turn pro.
Note: I'm working on photos/video of my favorite stretches. I would prefer to present that at this point, but it's just so damn time-consuming! It'll show up when I can grab the time (and a camera monkey) to film it.