Here's a piece comparing virtual manipulatives to traditional teaching without manipulatives, in the context of community college remedial courses:
Violeta Menil and Eric Fuchs, "Teaching Pre-Algebra and Algebra
Concepts to Community College Students through the Use of Virtual
Manipulatives", Improving Undergraduate Mathematics Learning, CUNY
Office of Academic Affairs, 2012. (Link)
Statistically significant improvements were found regarding exam performance and student attitude for prealgebra/arithmetic classes. None are found for either in elementary algebra classes.