What is com_set_option? As the title says, I'm wondering what is this command and why am I seeing a large amount of this query on my database? It's currently 13.30% of my total queries. I've tried googling this but there's not really any documentation on the subject.

Here's a part of the report done by mysqlreport:

__ Questions ___________________________________________________________
Total          17.43M     7.5/s
  DMS           8.58M     3.7/s  %Total:  49.23
  QC Hits       3.91M     1.7/s           22.42
  Com_          2.54M     1.1/s           14.54
  COM_QUIT      2.48M     1.1/s           14.21
  -Unknown     68.28k     0.0/s            0.39
Slow 10 s          17     0.0/s            0.00  %DMS:   0.00  Log:  ON
DMS             8.58M     3.7/s           49.23
  SELECT        6.05M     2.6/s           34.71         70.51
  INSERT        1.36M     0.6/s            7.80         15.85
  UPDATE        1.15M     0.5/s            6.60         13.40
  DELETE       20.35k     0.0/s            0.12          0.24
  REPLACE          61     0.0/s            0.00          0.00
Com_            2.54M     1.1/s           14.54
  set_option    2.32M     1.0/s           13.30
  show_proces  83.16k     0.0/s            0.48
  create_tabl  60.20k     0.0/s            0.35
It probably means that you ran a lot of commands that start with "SET something = somethingelse;"

I would say to set your general_log on for a short while on your dev environment and search for SET commands. It would probably be something to do with setting the server time.

http://dev.mysql.com/doc/refman/5.5/en/server-status-variables.html#statvar_Com_xxx