treeline - 5:06 pm on May 31, 2013 (gmt 0)
Typically, internal website links will not cause you any sort of trouble.....if you have a normal site, you know…a catalog site or whatever…. you’ve got breadcrumbs…you’ve got a normal template there…that’s just the way that people find their way around the site, and navigate, you should be totally fine.
The problems aren't going to be the standard web navigation styles Matt Cutts mentioned above. Even if you don't trust him, these are common to the top sites that are still ranking above you. They are very useful to real human visitors, who understand them because they've seen them a thousand times. Google has always been keen on things that are useful to real people.
In my niche, Penguin just cleaned out a whole bunch of garbage that I never understood how it got in. The real sites all stayed, more or less in order, sliding up a few slots into the newly vacated spots. No sites run by local businesses or enthusiasts vanished. Wikipedia also did well, getting to #1. They've got lots of internal linking.