The option flag you want is really just -threads and you would use it like this (for just one thread):

ffmpeg -i somefile.wmv -c:a libfdk_aac -c:v libx264  -threads 1 transcoded.mp4

However, there are quite a few subtleties that will raise your server load and ops time, such as rescaling, applying filters and final frame quality / frame rate - not to mention the fact that some VM architectures actually read and write everything twice (once natively and once virtually!!!)

Here are a few tips to get your speed up:

• use a queue, so that only one item is ever being transcoded at a time
• request smaller files from your users
• use the full horsepower of your machine by:
  • reading and writing from a ramdisk
  • switching to bare metal for transcoding tasks
  • use -threads 0