I have come to the conclusion that the best thing you can do to increase your mobility for squats is to squat more. I don't mean the bone crushing max effort style training of the likes of John Broz. Just some easy squats to grease the joints. I think 30-50% of max for a couple of sets of 5 reps is about right.
Squats will improve your mobility in the ankles, hips, and even shoulders in the case of the back squat.
For many people the squat just feels wrong when they go down into the hole.
-Their knees come forward.
-Their heels come off the ground.
-Their hips tuck under in the bottom position.
-Their arch is lost in both upper and lower back.
-The bar feels awkward on their back.
-Getting their hands into a position to hold the bar is a struggle.
This will cause them to do a lot of mobility drills and stretches to alleviate these problems. From a time efficiency standpoint I think they would be better served just doing the squatting move itself. The results would be better, and time would be saved. After a couple of weeks of doing the squat every day, or at least every training day, a lot of these problems just magically disappear.
So when should you do these squats? I think the best time to do them is as a part of your warm up. You do warm up before your workouts right? If you don't, you should.
Example warm up for a 200kg squatter:
5 min on the bike
Barbell Rows: 2 sets of 5 with just the 20kg bar
Overhead Press: 2 sets of 5 with just the 20kg bar
Front Squat: 1 set of 5 with just the 20 kg bar, then 2 sets of 5 with 50-70kg
Back Squat: 2 sets of 5 with 50-100kg