I downloaded the Faenza icon set and installed the "Dark" variant on my desktop.
However I only want the icons for applications (the ones that go in the Unity Launcher), I want all the other icons to remain stock. Here's a screenshot to illustrate:
Here's a possible method for doing this:
The top panel uses size 22 icons (places, apps). More details below.
Download the Faenza icon set from gnome-look.org or another site to a local folder. Inside you will see several themes: Faenza, Faenza Dark etc. Basically, the first one is the whole theme that includes all apps icons etc. and it does not depend on other themes, and the others depend on the first (so, if you use, for example, Faenza Dark then you must install Faenza as well).
So, unzip Faenza. You may want to rename the folder to something like Faenza Modified. Inside there is a file index.theme. It has extremely clear structure that tells the system where it can find icons for apps, system tray etc.:
[actions/16] [animations/16] etc.
Contains the description for all icon subsets.
So, basically, what you can do is look into subfolders, decide which ones you want to exclude, and delete them from Directories=... line.
Now, Compress the new folder, and Drag'n'Drop it onto the Appearance window (make sure that the icon set with the same name is not installed, otherwise delete it). It will install the modified theme and asks you whether you want to apply the new icon set.