All Transition effects but the Iris Wipe effect have a Transition Completion property. When this property is 100%, the transition is complete, and the underlying layers show through; the layer to which the effect is applied is entirely transparent. You typically animate this property from 0% to 100% over the time of the transition.

For an example of how to use animation presets to create custom transitions, see this entry in Stu Maschwitz's blog: www.adobe.com/go/learn_ae_stufilmburn. From this page, you can download the Film Burn animation preset, which adds film-like flicker to layers and adds a film burn transition to the ends of layers' durations.