Is hiding publications in CV a good idea? Here's my story:

I study computer science. When I started my master's degree, I had good research ideas and I wanted to publish them immideately (I now realize being in a hurry is the worst thing I did myself in my educational life).

My thesis advisor is a perfectionist. His philosophy is all or nothing. Therefore, he ignored my immature works and told me to get ready for my thesis only. He said that my thesis topic is one of the hottest topics in area and possible contributions to that topic would be huge improvement in my academic career.

But again, I was dissatisfied. So, with the ratification of my advisor, I published two conference papers with another professor. One is in ICCAE '12 and the other one is in ICKD '13. Those are not so good conferences, but still they are not in Beall's List.

Now, me and my advisor are writing a paper to submit a top conference.

Here's my question: Those publications are not a bit of scientific publications. They are barely at a level of senior project. When I'm applying to PhD, should I put those two publications in my CV or not? The acceptance notification of the conference is due to July. Until then, is it better to have no publications or two bad publications in my CV?
In most fields, expectations of publications are very small when applying for a PhD position. What the committee will be looking at is your writing. In most cases, they will have only the thesis to study but in your case, you will also have a few publications, including the one for the "good" conference. The benefit of all of these is that they show you have been active and pursued publishing your results. That the first publications may not be strong will not surprise most, after all one of the main goals of a PhD is to provide the background to be an independent researcher and publish.

You may be in a dilemma if your papers are of disputable quality since avoiding to list them may, if found out, look like you are trying to hide them; regardless of your original intent. 

To take this a step further: I think that adding comments on papers you think can reflect negatively on yourself can turn a negative to a positive. The reason is that you can show that you have progressed in your thinking to a point where you can be self-critical. This means that the comments you make have to be insightful and not just a list of excuses, in fact avoid excuses at all costs and provide good arguments showing your new insights.

So, think about how you can use your experiences (good or bad) in a positive way to show your capacity as a budding scientist. We all make mistakes, but not all learn from them.