If you wanted some program or "magic formula" to bring your squat up, then this isn't going to be what you want to hear. But too bad.
If I were you, I wouldn't employ any "advanced methods" until you were sure that your setup and form are perfect. If you're like a lot of people struggling with the squat, you might have poor hip mobility, poor glute activation, and weak and inhibited hamstrings and abs. If your back is rounding at all in the bottom position, you're losing a lot of pounds on the bar and putting a lot of compressive force on those discs. If your mechanics aren't already flawless, the easiest and most effective way to bring up your squat (especially in the long-term) is to improve them.
If you already have very good mechanics and a strong base (which I would define as a 2x bodyweight squat), then you should be able to employ more advanced techniques and programs such as Smolov and the Russian squat cycle. However, if you have poor mechanics, do yourself a favor and read every single Mike Robertson article on this site (really, they will help you tremendously). Don't try to fool yourself though - I've been there and it doesn't end pretty. As a 180-pound 18 year old, I was trying desperately to bring up my 285 squat, and attempted the Smolov squat cycle. Instead of ending with the 340 squat I wanted, I ended up with a hip injury.
Take a fair assessment of yourself and your weaknesses and work towards bringing them up in a systematic way, and your squat will go up. No "silver bullet" or magic program with the "Golden Number" of reps. Your squat doesn't suck because you've been doing 5x5 instead of 6x4. No method is going to help you increase your squat if you are not squatting properly to begin with, so worry less about methods and more about principles such as squat mechanics, and your squat will increase.