How low do you go ( squat)

What works for me is goblet squats. I make sure my weight is on my heels, not just on my toes.

I go below parallel, so I can really feel the activation in the hamstrings (the back of my legs), and the glutes. (My quads are much stronger than the hamstrings, so I'm primarily doing squats to strengthen my hamstrings. (The goblet squat is more of a full body exercise which also exercises my core, as opposed to the reverse leg curl which is more targeted.)

Doing squats on the Smith, I do not use a bench because I do NOT want "my butt hitting" the bench or anything, because that has too much potential for causing injury putting too much of a load on my spine and lower back. The key (for me) is feeling the activation in my hamstrings. My goal is maximize the amount of time my hamstrings are under tension.

If you're looking to strengthen hamstrings more, do more deadlifts. Squats tend to hit the quads more.

A common view is that full squats are bad for the knees because they require the knees to travel forward over the toes.

There is no evidence that having the knee travel forward over the toe is bad for the knees.

An analysis performed on cadavers found that the pressure on the knee decreases as the knee flexion angle increases from parallel to 120°... this would be the bottom part of the squat that scares many people!

It's an improper view. As you can easily break parallel without forward knee travel.
very true about the knee thing though. breaking parallel is actually better for your knees

I agree... I certainly don't think that squats performed with good form are ever bad for the knees, if anything building leg strength through squats will help prevent injury.

Make you run faster, jump higher etc. etc.

Maybe I'm doing it wrong...I used dumbells last night and every time I went lower than parallel, I heard serious crunching in my knees. I'm trying to focus on putting the weight on my heels, though.

If you're looking to strengthen hamstrings more, do more deadlifts. Squats tend to hit the quads more.

Squats are primarily hamstrings, hips and glutes depending on how you do them.
Quads still get some good activiation but they definitely aren't the primary mover.

I'm really inflexible and have always struggled going really low with my squats. Basically im wondering if this will this hinder my progress? (I'm doing stronglifts presently, 7 sessions in) Opinions pleaseeeee!!

You really need to get to parallel with the Back Squat. Work on your flexibility and mobility. Work on things to make your lower back, hamstrings, and hip flexors more flexible.

with flexibility issues, it might help to widen your stance a bit and have your toes pointed a bit outwards. just make sure you are essentially splliting the floor with your knees and he knees are going in the same direction as your feet

Definitely get to parallel. If you're having trouble with this see if there is a box or bench that you can pull into the squat rack and do Box Squats. Just make sure that the box or bench is low enough for you to achieve parallel. Box squats are a good way to teach form and it's actually a great version of the squat. Some powerlifters train box squats almost exclusively.

I could adapt this to my Pistol Squats, squatting down to a chair seat or something lower until I can squat back up from the heel - thanks.

Body By You by Mark Lauren has this exercise - one legged squats "box" squats. I had been doing them because, like you, I could only do one legged squats with the leg behind.

They felt like an effective exercise, but I found that they hurt my knees too much . I've gone back to barbell squats for now, and will maybe come back to working towards pistol squats when I've lost a bit more weight.

However, one of my friends here suggested two-legged squats with feet together as preparation. I'm not sure about these as they seem to easy (and I don't want to do hundreds of them with my dodgy knees), but maybe they would be useful? I thought they might help because obviously your body is balanced quite differently if the weight is over one leg rather than two legs in a squat position, and this is closer to a pistol squat than squatting with legs apart.