It is very common that themes provide a background image for the panel, which is most of the time a simple gradient. Currently, such an image is displayed exactly the same way regardless of the orientation of the panel. This works well for horizontal panels (the way theme authors meant it to be used), but not for vertical panels, where the gradient is repeated in an ugly way.
The default theme of Linux Mint Debian Edition is a good example : run a fresh live USB, move the bottom panel to the left or right and here you are.
A temporary "solution" is to disable the background image completely and use a plain color instead. In addition to not being a real solution, it is only half working since some applets (window list for example) keep using the theme's default background image. I don't know if this is a problem of mate-panel or the applet itself.
There are 3 possible good solutions I see :
Provide an additional option in the "Background" option tab named "Rotate image". It would offer either "90° clock wise", "90° counter clock wise" and "default" (possibly even "mirror" or "180°", while we're at it). The default for an horizontal panel would be "default" (i.e. no rotation), left would be "90° CCW" and right would be "90° CW" for example. The problem is that it should be configurable by the theme itself (maybe the authors will want to rotate "90° CW" for the left panel, for example, or not rotate at all), and I don't know if such a thing is possible.
Provide a way for themes to offer different background images depending on the orientation of the panel (i.e. one image for horizontal panels in general, one image for top panels, one image for left panels, ...). I am not familiar with GTK themes, so I don't know if such a change would break existing themes. It shouldn't though.
Like 2), and allow defining the background as a gradient (prevents the gradient from repeating when the panel is too large).
Edit : I can only test Mate 1.2, maybe this issue is no longer present in the latest version.
@stefano-k - Please close this as #157 also describes panel background require rotation.