Working out when sore/stiff

I personally recommend "easing" into fitness rather than going form doing pretty much nothing to all out balls to the wall workingout 6-7 days per week. It's a recipe for injury. For the most part, you don't really need rest days from things like the elliptical and what not...but early on, it's probably not a bad idea to cut yourself some slack.

When I got back into fitness I only went 3x weekly...one of those days was a run/walk and the other two were just walking. I slowly built up to the point where I was running each of those three days and walking on the days in between..a year later I have no problem taking a 3 mile maintenance run in the morning or afternoon and then heading out on my bike for 15- 20 miles later in the evening and getting up and doing it all over again in the morning...but buiding up your fitness takes time.

Are you stretching pre and post workout?

I'd say keep the legs moving, but don't push it. I was really sore after my kickball game last Sunday, but going for a run on Tuesday (when I was most sore) helped the pain, and it was gone by the time I was done with my run on Wednesday. At least get a walk in on the treadmill or outside. You don't gotta go nuts, just use them. And yes, make sure you stretch post-workout, after you're warm.

Do something else stiffness in the knee is usually a sign of pending injury I speak from experience , do some weight training

It's a balancing act. On the one hand you absolutely, positively, should not work out injured. Rest for as long as it takes to heal, then add a week.

On the other hand, if it's just DOMS, then get 48 hours rest and then get back to it. If you wait for DOMS to go away completely before working out again, they will always be as bad. But if you give it 48 hours rest, and then go into the next session still a little sore you will find two things happen -

1. The workout helps the DOMS to go away.
2. The DOMS will not be as bad next time.

I also agree that you should gradually build your activity level, to minimize chance of injury. Personally, my build up looked like this over the course of a year -

1. Walking 15 minutes everyday, building up to 30 minutes.
2. Started C25k program 3 days a week, with gentle walking on the days in between.
3. Adding a machine weights program onto the days between C25k. Rest on Sundays
4. Graduated C25k, started running 5k M,W,F while still doing machine weights Tu, Th, S. Rest on Sundays.
5. Graduated from machine weights to free weights. Now running 5k M, W, F and doing Strong Lifts Tu, Th, S. Rest on Sundays.
6. Started increasing my running. 10k on Mon, Intervals on Wed, tempo run on Fri. Strong Lifts Tu, Th, S. Rest on Sundays.

Even with this gradual ramp up, I still had a minor injury to my IT band once, and to my back once. Both of which put me out of action for two or three weeks. I dread to think what would have happened if I hadn't gradually worked my way into it.

I wouldn't recommend working out stiff. Just throw a towel over it until it goes down some and isn't noticeable.

This is why you switch up body parts from day to day, and also take 1 to 2 rest days per week. You didn't get out of shape overnight and you're not gonna get IN shape overnight. I see too many people start strong and overdo it, and then quit out of frustration or injury. Slow and steady wins the race...and make sure you're STRETCHING!

Scivation Extend is a great drink to drink it stops soreness.
You sound like you are getting sore hamstrings. Do some good hamstring stretches after the workout to cool down, and maybe do a pilates or yoga class once a week to improve your flexibility.
Don't stop as you will work the lactic acid out of your muscles by doing another workout.

It's my understanding that there is no consensus on whether stretching helps. Some studies show that it helps, some show that it makes no difference, some show that it makes injury more likely (that last thing probably due to people believing they're magically immune to injury if only they stretch).