One of the best parts about long runs during training? The day of rest that comes after. You could take the day off completely (I won't judge you now; I've done that before), or go easy on the mileage. Really, it's about listening to your body and doing what it needs.
I stretched extensively yesterday after my long run. However, my right piriformis still felt tight (or so I think that's what it is -- the longer I sit, the more pain I feel, which is indicative of piriformis syndrome), so I opted for yoga. My last chiropractor had recommended it as a means to develop flexibility and core strength. When I realized that my gym membership included yoga classes, I was toward the end of my training for the NYC Marathon, and needed all of the stretching/flexibility help that I could get. So I tried it, and I've been going fairly regularly since then. I've even convinced a few classmates to go. (It's possible that the improved flexibility from yoga helped me PR in NY, but I can't confirm that one.)
My gym has a great Vinyasa yoga on Monday evenings, so I went there. (If you don't have a gym membership, or belong to one that doesn't offer yoga classes, scour sites such as Groupon or Living Social. They always seem to have deals for yoga classes!) It was quite beneficial, especially the pigeon pose! (Note: I went for a massage recently, and the massage therapist told me that my iliotibial band was really tight, so it's possible that this is my issue. It's also possible that both areas are tight.)
Unless you're an athlete, are well-versed on human anatomy (no lewd jokes, people!), and/or have had these issues before, you're probably wondering what I'm talking about. Well, today's your lucky day, because I (with the help of my undergrad Anatomy textbook -- I KNEW there was a reason I saved it!) have a brief lesson! Are you ready for this??
The piriformis is the muscle that originates from the sacrum and inserts on the greater trochanter (head) of the femur, and is responsible for laterally rotating your thigh. (You know all those times you twist your thigh outward? Go thank your piriformis.)
The iliotibial tract (band) is a thickening of the fascia lata (sheaths of fibrous tissue) that extends from the iliac crest (part of the pelvic girdle) and attaches to the lateral condyle (upper portion) of the tibia. The gluteus maximus (responsible for laterally rotating the thigh) and tensor fasciae latae (responsible for medially rotating the thigh, or rotating it inward) both attach to it. It helps stabilize the knee during extension and flexion, meaning that it's used constantly during running and walking. It can also get irritated from overuse. (There's a reason why IT Band Syndrome is commonly referred to as "Runner's Knee!")
But I digress. For further information on either part or syndrome, consult a trained professional, book, or Google.
Source: McKinley, M. & O'Louglin, V.D. (2006). Human Anatomy. New York: McGraw-Hill.