Training the hamstrings is pretty straight forward. They serve a simple purpose--to pull your leg back with respect to the rest of your body--and that's how you work them.
A lot of the quad exercises will put some stress on the hamstrings, but I think you should reserve an exercise--or two--that work only the hamstrings. If you develop an imbalance between the quads and hams you can gaurantee yourself a pulled hamstring further down the road.
On to the exercises...
Machines that operate with cables attatched to the movement arm tend to distribute the weight more evenly through the movement and for that reason I recommend them before simpler, lever-based implementations.
You won't be able to do as much weight on this as you do on leg extensions. If you've never performed this movement before, use about one third of the weight you use on leg extensions.
Lie face down on the machine and hook your ankles behind the pad. Grab the handles below you to give you more leverage in the pulling motion. Your knees should be just a tad beyond the edge of the bench so that you can freely and comfortably bend them.
Curl your legs up until the pad touches your butt--or gets as close to it as is reasonably possible. Lower it back down slowly. Barely allow the stack to touch the bottom before raising it back again.
Hamstrings.
This is my preferred hamstring isolation movement.
Use less weight than you would in a regular dead lift. Much less. Keeping your legs straight, bend down and pick up the weight. Your knees should not be locked, but keep them as straight as possible without locking them. Straighten up and wihtout bending your arms. Lower the weight back to the floor and repeat. Remember to wear a belt for this exercise because it does put a lot of stress on the lower back.
Hamstrings, lower back.
If leg curls just aren't clicking for you then this is the movement to turn to.