So I tried my first real squat today and I couldn't stand that bar cutting into my shoulders. My neck still kind of hurts. I've just been using the leg press machine for about 2 years and I've gotten some gains on that and I do about 300 lbs. I'm not sure how much real weight that equates to but I tried 125 lbs with the real squat and, yeah I can't deal with that bar on my shoulders. I did some hack squats on a free weight machine instead.

So, what alternatives are there. I do prefer the "machines" that are more like free weights in that you add weights and you just push the shoulder pads up, no cables or pulleys (I don't know what these are called). Should I combine some different machine leg workouts to get the equivalent of a squat?

The rest of my workout is dips, pull-ups, leg raises and shoulder presses and they seem to be working. I just need a safe leg workout that I won't hurt myself with.

 I am definitely not a weightlifting type, but for that reason I've looked at technique closely.
Some people suffer with lower back and/or knees which puts them off squatting, but you should definitely not be feeling distress in your neck. It is almost certain that you are holding the bar far too high on your shoulders if this is happening.
Something that may help is a cambered bar -but these are rare.

If you are just leg-pressing, might be worth including deadlift.
The closest machine to the squat, I have heard, is called the 'Tru-squat' machine , but these are also rare.

I'll have to try those Bulgarian squats. I think I can handle those. I'm pretty sure my form was fucked when I did those squats. I still have a knot on the back of my neck that's pretty sore. Do the bulgarian squats cover all the muscles that I need to hit though?

the alternative to the back squat is the front squat.
If that still bothers you, all the dumbbell variations: dumbbell front squat, Goblet squat.
If that still bothers you, Bulgarian dead lifts.

Feeling light headed is pretty common when doing squats I think, at least if you're pushing yourself at all.

If your neck is hurting, this is often indicative of a grip that is too wide. Narrow your grip, bunch your beefy trapezius muscles up to make a pillow for the bar to sit on.

Also, be wary of squat machines. They often force your body into un-natural alignment in terms of knee and hip position. They are geared towards people with low flexibility. Using a squat machine robs you of all of the benefits of free weight squats. Namely, activation of all of the joint and core stabilizers.

Also, if you are going to be doing squats, make sure you work on ankle flexibility. Contrary to popular belief, popularized by nautilus machines in the 80's/90's full squats are not bad, and your shins should not remain perpendicular to the floor.

http://www.youtube.com/embed/ebUT4G6Akk4

This guy has poor ankle flexibility, notice how is butt and hips starts to squeak out behind him? This is the hallmark of a "typical backsquat". It is hard on your spine, knee's and neck. This is a typical "power lifting" technique and does not infact exercise the entire range of motion of your legs. It is however, easier.

http://www.youtube.com/watch?v=RzT1lY-q-hg
This guy has pretty good technique, although he is crashing at the bottom a bit. Notice how as he bend his knee's the angle between his feet an shins increase so that hit butt and hips move directly up and down? This helps insure that the force vectors acting along your spine remain straight up and down. This is a good thing, as your spine and joins are NOT designed to handle lots of shearing or lateral forces. Notice the intese Quadriceps femoris development along with sick gastrocnemius (calf muscle) development? You can't get that without proper full squat technique

Notice how is neck isn't pushed too far forwards, his hands are in such a position that his traps are bunched up to form a pillow at the back? This will limit pain during the exercise. There is also a certain amount of "just getting used to it" as well.
 
This is coming from an ex Olympic style weightlifter with a degree in Kinesiology and Physiology, so keep in mind that I come from a functional muscle vs beach muscle background. 

This is kind of an old thread that has been resurected but if you are planning on not doing squats because it hurts your shoulders, you should start lighter, do it more often, and get used to it.  It does get better.  The combination of front squart, RDLs and hip thrusts is a good replacement for someone that can't back squat, and are all good to do in their own right, anyway.  Back squats are still the most efficient overall exercise there is, and it is worth your while to become aclimatized to the weight on your shoulders. 

I do kettlebell training - still just a beginner, but I do one of the basic exercises that include a squat-like motion while not being hard on joints or the shoulder. The reason is that as you swing the kettlebell back and forth, you're not actually lifting the weight but trying to create a counterbalance to stay in place and not fly away with the weight So it makes the muscles work very effectively, but doesn't actually put weight on the joints.