I can offer three films to consider:
1) Molecular visualizations of DNA
2) Malaria lifecycle - part 1, part 2
3) other films at WEHI
Links are provided by Rod Page's excellent blog, iPhylo. I saw the malaria films as presented by their creator, Drew Barry. Amazing!
A fourth example added in edit: Cold Spring Harbor's DNA Learning Center has much to offer, including Biology Animation &
3-D Animation Libraries. Topics include Cloning 101, Cycle Sequencing, DNA Arrays, DNA Restriction, DNA Transformation, Gel Electrophoresis, GeneChip®, How Alu Jumps, Polymerase Chain Reaction, Sanger Sequencing, Stem Cells Lines, and animation on the DNA molecule, Transcription and Translation, Replication, Experiments & Techniques, and Disease and Mutation. These all seem like very good molecular biology topics.
*Added in edit on 17 Oct 2011: There are a few dozen links to various education resources provided by the National Human Genome Research Institute's Online Genetics Education Resources page. Some of these point to sites like CSHL's DNA Learning Center that host films.*