SQL date format convert? [dd.mm.yy to YYYY-MM-DD]

Since your input is a string in the form 03.09.13, I'll assume (since today is September 3, 2013) that it's dd-mm-yy. You can convert it to a date using STR_TO_DATE:

STR_TO_DATE(myVal, '%d.%m.%y')

Then you can format it back to a string using DATE_FORMAT:

DATE_FORMAT(STR_TO_DATE(myVal, '%d.%m.%y'), '%Y-%m-%d')

Note that the year is %y (lowercase "y") in STR_TO_DATE and %Y (uppercase "Y") in DATE_FORMAT. The lowercase version is for two-digit years and the uppercase is for four-digit years.