A long time ago, I used to be able to touch my toes. A decade of no exercise and a sedentary job took care of that.
One of the things that I wanted to work on this year was comfort, and flexibility and core strength are the key to on-bike comfort. For the past several months I have been diligently doing stretching, isometric exercises, and yoga. The areas that I am specifically targeting are my lower back, hamstrings, calf & ankle flexibility, and torso flexibility.
It took about five months, but I recently was able to touch my toes again. I have also noticed more comfort on the bike, especially when twisting around to look at traffic behind me.
I'll continue with these exercise even though my riding is ramping up for the Lewis & Clark Ultra, I don't see it as something to be done instead of riding but in addition to.
There are a lot of online resources for yoga and stretching ideas, but one book & DVD that I found very useful is Yoga For Bicyclists. I mostly use the first workout, which is geared more towards general flexibility. The second set of exercise is more strenuous than I can handle.
The DVD is helpful, especially at the beginning, because you can just follow along with it; my daughter really enjoys doing the yoga with me too, so that's an additional benefit. The book is helpful if you want to really customize your program, you can just browse through and pick the poses that you think will provide the maximum benefit.
The important thing is to evaluate areas that need to be worked on and develop a regimen that will help you to improve. Also bear in mind that you won't see overnight progress, depending on your age and other fitness factors you may need to continue your program for quite some time before seeing any improvement.