jimbeetle - 6:03 pm on Sep 19, 2013 (gmt 0)
If links are not reported as "manual actions", should I just assume they may look bad but aren't bad?
"Manual actions" can be related to unnatural links, but Penguin is algorithmic, so no notice will show in Webmaster tools.
How can I tell what backlinks hurt or help me?
Any spammy links built by your SEO companies should be easy to spot. You can eyeball them or use a tool such as the Boykin boy's handy-dandy backlink checker tool for Penguin and disavow analysis [backlinks.webmasterworld.com]. It's not the be all and end all, but it's a pretty good place to start.
Of course, the above is based on the assumption you determine it is a Penguin problem.