Need a form check...
 

When I first started squatting, I had my feet at a neutral angle. I squatted and got a good bit of hamstring pain, and it was suggested that I "toe in" a bit. I did the next week with my feet straight forward, and had to take the week after that completely off because my knees hurt all week. I went back to the neutral angle today, and, surprise surprise, my hamstring pain is back in full force. Here's a video of one of my warmup sets, is there anything visible that I'm doing wrong? Getting sick of this:arg:

...my apologies for the background music, as well as the sideways video.
http://youtube.com/watch?v=lCi8Q1QtL9c

It looks like your legs are too close together but it's kinda hard to see how far apart your legs truly are from that angle. Other than that, it looks ok.
So, how far apart are your legs?

Just a little over shoulder-width apart

u need to have a tighter arch........

Is that from your heals or toes? If your toes are pointed out then you need to make sure your shoulder-width is from your heals.

Speaking of which, looking at your vid again, when you go down, it looks like your heals are coming up a little. I would work on arching just a little bit more and focus on driving with your heals. If you feel off balance then you have to move your legs around to get into a better position. What I find works is when you squat try lifting your toes off the ground a little. NOT rocking back on your heals, just a small lift, so you can feel the weight shift back to your heals and on the balls of your feet. This is another good technique for BB Cleans and Snatches.

Yeah your weight is definitely shifting to the toes. The degree of forward lean you have is a clue to that as well. You are probably somewhat quad dominant...a strength imbalance that could lead to the kind of strain you are feeling in your hams. Also you should work on flexibility a little since you may be generally tight in the psoas/quad region (front of hips and thighs) although general hamstring flexibility needs to be maintained as well.

What are some lifts that would help even out a quad dominant structure? And I just tried a few "free" squats trying to keep my heels down...I can see an improvement in the mechanics of my squat already. I'm hoping the hams will be feeling alright for Wednesday, I've taken a lot of time off of squats and DL's already (all of last week). Besides, I've grown quite fond of them :weighlift:

Well with what you are doing I'd say glute/ham raises would be a good addition. You also may be able to do some Romanian deadlifts. One or the other. I'd vote for the glute/ham raises.

The stregth ratio to prevent injury and strain is minimum 80%. So in other words that would be something like doing extensions with 100 pounds max and leg curls with 80 lbs. But I think it can be as much as a 1 to 1 ratio (although I'm not sure). It's hard to test in reality though.

Going lower may be of benefit because it will allow the hip extensors (including the hams) to fire optimally. And of course fixing your form as Dave pointed out is going to help since transferring the weight forward is firing the quads and putting the hams in a weak position, causing them to strain.

The weight is definetly at your toes as well as your knees are hanging way past the tips of your toes as well.

What Eric said.
Also, another trick I find that helps to find your squat position is take an empty bar, set up the squat rack pins right below where you are at dead bottom of the squat, for safety. First, squat down withOUT the bar like a normal squat and see if you can hold the position, at dead bottom, for a 10-15 count. If you have discomfort, adjust while you are at the bottom. Then after doing that 3-5 times see how it feels with JUST the bar and the position you think is good for you at dead bottom. I don't recommend adjusting your position too much at the bottom when you are using the bar. But the pins are there just incase the bar is getting too much. Also, use the toe trick at the bottom this will help your form stay constant throughout the movement.