I'm currently interning at a small startup, where I plan to pursue as a job in the coming year. How does this affect my college applications for a MS in CS in 2015? Does a job at a MNC make a difference?

I think you are in a good position. Trust me. I have worked 8+ yrs in an MNC. After 4 months there, I got frustrated since the learning curve hit a plateau. I went to my Vice President and asked for better opportunities. He told me I was too much in a hurry and not patient. At that time, the opportunities of startups was not much probably and also not visible to me. So, I continued for 8 yrs.. Now, I run a startup. I am sure the learning curve is so steep that you are in a much better position. In fact, I would even tend to think that an MS is not so essential, especially in computer science. Check out the below story. http://www.ndtv.com/article/world/commentary-how-to-get-a-job-at-google-486872?pfrom=home-topstories I would tend to agree. Technologies are changing so fast, at least in software side that an MS may not be the best option. You have great courses available at Coursera, Edx etc. Why not look at that? Your Return on Investment (ROI) will be much better. From what I know, if you are not onto technologies which are high investment stuff which only universities can get access to you, these courses are better. Good Startups will give you good people to work in any case. Of course, I am not saying that an MS is of no use. If it's a great university and you are going to work under great profs, you should go for it. Good luck.