Flashbacks are one of the most interesting aspects to film, in my opinion. There are all sorts of ways to do them, based on what information you want to give the audience and what you want to convey during it. Here are some of the ways I've seen flashbacks done:
Wavy lines go across the screen as it fades to the flashback (and fades back to the present time), as seen in Waynes World.
The flashback is in black and white, contrasting the color of the present time (I think this can be seen in Kill Bill, but I can't remember).
A flash of light transitions between the present and past.
A normal transition to the flashback, but a subtitle lists the time of the scene (this is also common for moving forward in time as well)
There is a normal transition and the audience has to pick up on special clues in the frame to know it's a flashback (i.e. someone who is dead current time is alive, or a certain background, etc).
If you want to check out a great flashback/flashforward movie, check out Primer. It's a great movie for all student and indie filmmakers as it was made for only $7000 (most of which was spent on film and film processing) and went to Sundance and got the Grand Jury prize. I have to warn you, however, that you probably won't understand the movie until you watch it 2 or more times!
