Well, basically the oven takes longer. In both cases you'd make up your medium over the stove first. Many people have written very good information about the different methods of sterilisation, and I doubt I could improve on the info they've provided. I recommend taking a look at this site as a first step:
Lotte & Thomas Orchids
Lots of info about different sterilisation methods, media preparation, etc.
Also, try searching on YouTube for 'microwave sterilisation of orchid medium'. There are some very good videos there.