Is hiding publications in CV a good idea?
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.