Since you still have 2 years until you apply, I’m sure you’ll do lots of CS-related things between now and then. I would hesitate to list things you haven’t updated since middle school, because of the general “middle school doesn’t count” guideline. So, making more apps yourself and with partners sounds like a great idea.
We haven’t gotten to the point where my son would be filling out applications yet (Class of 2017), so the following are just ideas without having dealt with applications yet. Perhaps others with more experience at applications can comment. (My son’s current plan is to major in physics/astrophysics, but he does a lot of programming.)
He took the AP CS test before high school, so doesn’t have that class on his transcript. However, I think that he will end up with one or two CS classes from a community college on his transcript within the next year and a half. If you don’t have a local community college with good CS classes, you could take a Coursera/edX/etc class to have a non-transcript class to list. Personally, Data Structures was one of the most useful classes I’ve taken, and I’m not even a programmer. (I’m a technical writer who writes for programmers.)
He has two GitHub accounts, one under his realname and one under an alias. Projects that he feels are “complete” and good (or that he wants to force himself to make so) he puts under his realname account. I think the plan is to point to that somehow on applications. I’ll bet CMU would be cool with that; don’t know about the others.
He works on things that could loosely go into an “art supplement” which a number of the elites accept. He’s using Blender for 3D modeling and has some good results so far, and hopefully they will get better. One of his ongoing hobby projects generates art procedurally and somewhat evolutionarily, so sample output from that along with a pointer to the GitHub project is possible. Screen captures from your apps could go in something like this. I think he has a Tumbler account going where he posts stuff like this; I don’t know whether that will be something he wants to share, however.
I’ve heard that there’s an “additional information” section in the Common App and that some colleges (but not many) let you submit a resume. Those would be a good place to list the languages/operating systems/modeling tools you are proficient in and to briefly describe significant CS projects you’ve worked on. Contributing to open source projects, as mentioned by @maaz97, sounds good, especially with a significant lines of code statistic.
Is there a programming club at your HS or could you start one? Mentoring other kids at programming is an EC that adcoms are familiar with, while GitHub and open source stuff may not be familiar to adcoms at places that don’t admit by major. My son is on a fairly successful CTF-style hacking team. Again, that would sell well at CMU; not sure about the others. He’s trying to open that team up to more kids at school as a club, rather that keeping it a secret for a few kids.
I have no idea what he’ll write for his essays, but I’m pretty sure programming will be mentioned, because his programming skills have been so useful in the physics research he’s doing and loves. I wouldn’t shy away from talking about programming in your essay(s), but you might need to try a few approaches before you find one that works.