I have seen this question, but I believe the situation has changed a lot with the recent Panda updates.
I have created a set of category pages to facilitate navigation on my site. It is a proper hierarchy with no duplicates. However, these pages contain mostly navigation links.
Could these be considered thin content by Google? Or, is there a good reason I should mark them as noindex? Or should let Google index them?
After running some tests, I can confirm for sure that letting Google index my category pages triggered a silent penalty where all my indexed pages where not matched to user queries anymore. I had a high rate of those pages on my site.
First, I marked them a 'noindex,follow', but it had no impact, since these pages where still in the index. I decided to use the 'remove URL' feature of GWT aggressively to blast those pages away from the index. It worked. Within a day, Google was starting to match remaining pages with user queries again.