"That special someone," most commonly refers to someone that has done something meaningful for you/another individual. The phrase could also point out to someone who by which has special skills and/or abilities for a certain manner, or even use it in an anonymous manner to a group of people for that only the person it was directed to will know who they meant. Sometimes it can be used sarcastically for someone who by which is the, "oddball," or literally the, "special one," out of a group or in any other circumstance.
