I was an happy user of Noteburner on XP 32 bit but then I upgraded to Vista 64 bit. I contacted their support and they confirmed it does not work but they don't have any date for a new version.
That depends on your needs. I note that Noteburner also undoes DRM, and this requirement may narrow the field quite a bit. It might be that your best solution will be a combination of products, rather than one.
See Gizmo's article Best Free Audio / Video Format Conversion Program which discusses the merits of FormatFactory, Pazera Video Converters Suite, Quick Media Converter, MediaCoder and SUPER. One or more of them them should match your needs.