A recent paper in PLoS Computational Biology has an excellent list of freely available resources for online learning. Most are full university courses (of varying levels) that have been made available by major US institutions (Berkley, UCLA, MIT, Yale…).
Searls DB (2012) An Online Bioinformatics Curriculum. PLoS Comput Biol 8(9): e1002632. doi:10.1371/journal.pcbi.1002632