Pause squats, absolutely. Box squats have very little carryover for most people who are raw squatters. Pause squats help my depth and nail my legs with extra TUT. They also allow me to get lots of good work in with lighter weights. They even relieve some of the pressure on my knees from trying to maximize rebound on my normal back squat.
Pause squats are hard and they suck. Most of the time the version that sucks more and is harder is probably the one you should be doing.
If/when I start using equipment again I'll mess with box squats. Until then, I'll stick with pause squats and kettlebell swings to build my squat.
Current PRs at 242- 495, 345, 585, 1425