Sound design and color grading are often used to distinguish flashbacks from real time. It really depends on the look and tone of your film as to how you want to approach it.
A few ideas are warmer tones, vignettes, softer image, film grain, or directional highlight blurs. Use some sort of whoosh or drone sound effect to snap in and out of flashback. There is an
old tutorial here on Creative Cow that shows how to replicate the look of the flashbacks in the Bourne movies.
