Planet13 - 12:57 am on Dec 22, 2011 (gmt 0)
There are much better, more sophisticated ways to help "guide" the flow of page rank through your site than trying to sculpt it with noindex or with robots.txt.
This is established by how the internal links are set up, where they appear in the page, what anchor text is used, how relevant the material is, etc.,
However, done incorrectly, one can incur an Over Optimization Penalty (commonly referred to on these boards as an OOP).
It usually takes a good deal of messing up a site to get such a penalty, but some sites might be "on the edge" of getting a penalty without realizing it, so a simple mistake might push it over the edge.
(This is based on the assumption that Over Optimization Penalties are cut and dry - you are either penalized or you aren't penalized. As far as my understanding, in terms of over optimization, there isn't any "kind of penalized" state. Further, this comes from me seeking out and asking DOZENS of people who have incurred an over optimization penalty - I haven't incurred one myself (touch wood).)