Yes, it's called pane-level skinning. I will explain it in .ascx method versus HTML, but it can be done either way.

To make pane-level skinning work, you have to determine at design time if the skin package will be installed at Host level or at Portal level.

Here is an ascx code sample for a content pane, skinned at pane-level:
<div id="LeftPane" runat="server" ContainerType="G" ContainerName="EasyContainers" ContainerSource="Invisible.ascx" />

So, the parameters are:
ContainerType ~ this can be either "G" for global (a host skin installation) or "L" for local (a portal skin installation)
ContainerName ~ this is the folder name that holds your container
ContainerSource ~ this is the file name of your container

In HTML method skinning, these parameters are added to the .xml file.