First-authorship was taken by my Master's supervisor; how to strengthen my PhD application? I have two papers in CS published during my Master's studies. The idea, the experiments and the writings were done all by myself, but my previous supervisor took the first-author place forcibly. 

I am planning on applying to US PhD programs. My questions:


  
  Generally speaking, will these publications still carry the same
  weight as if I were rightly listed as the first author? 
  Are there any general strategies I can use to maximize the impact that
  these publications will have on my acceptance?
(I assume here that you're talking about admission to PhD programs.)

I'm not in computer science, so I can't speak with authority.  We have a number of users here who are in US computer science departments and maybe one of them can step in.

However, I would think that first-author publications would not be essential for admission to good PhD programs in the US.  Keep in mind that in the US system, most students would enter a PhD program immediately after their undergraduate (bachelor's) degree, without doing a masters first.  These students would not necessarily have any publications at all.  The admission committee would expect somewhat more from a student with a masters, but I'd think any publications, first-author or not, would be a pretty good sign of your research ability and preparation to start a PhD.

Another thing to note is that recommendation letters are very important for admission to US PhD programs.  If your advisor writes you a letter which speaks highly of the work you did, that should help your application a lot.