This is the incredible Harvard animation that tours the inside of a cell. I either showed it to you or TRIED to show it to you on day one! I mean who needs to go to the movies? http://www.aimediaserver.com/studiodaily/harvard/harvard.swf
Here is a good visual for the way that a simple buffer (acetic acid / acetate ion) works to moderate pH levels when an acid or a base are added. http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/buffer12.swf
This is a cute animation of glycolysis. Try the quiz at the end for fun! http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html
An animation of Krebs cycle and a quiz for you to try! http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html
This shows how NAD+ acts as an electron carrier in the cell. http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_nad__works.html
Animation of the electron transport chain. http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html
A detailed look at ATP synthase! http://vcell.ndsu.edu/animations/atpgradient/movie.htm
Detailed look at electron transport chain. http://vcell.ndsu.edu/animations/etc/movie.htm
Photosynthesis http://vcell.ndsu.edu/animations/photosynthesis/index.htm
Calvin Cycle http://www.science.smith.edu/departments/Biology/Bio231/calvin.html
DNA Replication http://www.wiley.com/legacy/college/boyer/0470003790/animations/replication/replication.htm
Transcription http://www.johnkyrk.com/DNAtranscript.swf
Translation http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf
Action Potential http://bcs.whfreeman.com/thelifewire/content/chp44/4402s.swf
Synapse http://www.bishopstopford.com/faculties/science/arthur/synapse.swf
Gel Electrophoresis - follow the prompts... http://www.dnalc.org/resources/animations/gelelectrophoresis.html