To miss_em, the Smith Machine allows you to press in a straight fixed line. You need to change the working plane to a more 3 dimensional plane. Use DB at different bench angles on different days and after a cycle with them, go and test yourself on the Smith Machine. You should see an increase.
As for free squats, do you have a strong back and core, good hamstring and glute development? Are you good at deadlifts with knees behind toes? Can you perform split squats in a deep ROM? Do you have good flexibilty in the hips, knees and ankles?
If you want to free squat by yourself, then make sure you work in a power rack with safety pins. Start with a standard BB, a small ROM and work your way down till your skill and confidence levels rise. Practice squatting backwards so you put less stress or shear on the knees. I suspect that is why you like the Smith Machine.
If you do not have access to a power rack, then try Smith Machine Split Squats keeping your leading knee behind your toes and emphasise a deep stretch of your quads and glutes. You can also do them with DBs and rear foot elevated on a bench or high step.