Manual penalties will indeed show up under Manual Actions in Google Webmasters tools. However most cases of rankings stagnating or dropping are connected to algorithm changes, however now with Penguin 4.0 just being launched it seems, that's not often the case anymore.
So if it turns out that you've been building links enthusiastically and your rankings don't improve it could be that you're focussing on the wrong type of links, as bad links don't hurt your rankings anymore, they are just being ignored.
