Qualifying for CTY isn't likely to directly affect a college application (it's too far in the past to really make much difference by the time a kid applies). What might be more important is whether he uses the CTY courses or any other courses to supplement his education and pursue his passions over the course of middle school and high school. CTY and other similar GT-oriented programs can (1) provide a real peer group for gifted kids, which they often don't get other places (2) pave the way for them to explore and learn in depth. Both of those experiences may directly or indirectly help a college application.
But definitely (and this is speaking as a person who has done admissions interviews for MIT for over a decade) do not have your kid take courses for the purpose of looking good on an application. He should do things he is interested in and will learn from. He should pursue his interests with seriousness and drive and persistence and curiosity. If he does that, it will show through on an application, regardless of whether any specific program is present on the resume. If he's doing things to look good on the application, let me tell you, interviewers and admissions committees are looking for that and we tend not to like it.
