Welcome to the Q&A Forum

Firstly, please don't assume that you've been hit by Panda. Find out. Indexation count is generally not a good basis for assuming a penalty. Was there a traffic drop around the date of a known Panda update? Check this list. https://moz.com/google-algorithm-change . If the date of traffic drop lines up, you might have a problem. Otherwise it could easily be something else. How many links does your site have? Google indexes and crawls based on your authority. It's one area where it doesn't really matter where the links go: just having more links seems to increase the amount your site is crawled. Obviously the links should be non-spammy. Do you have a site map? Are you linking to all of these pages? It could be an architecture issue unrelated to penalty. If it is a Panda issue: generally I think people take the wrong approach to Panda. It's NOT a matter of page count. I run sites with hundreds of thousands of URLs indexed, useful pages with relatively few links and no problems. It's a matter of usefulness. So you can decrease your Panda risk by cutting out useless pages - or you can increase the usefulness of those pages. When consulting I had good luck helping people recover from penalties, and with Panda I'd go through a whole process of figuring out what the user wanted (surveys, interviews, user testing, click maps, etc.), looking at what the competition was doing through that lens, and then re-ordering pages, adjusting layout, adding content, and improving functionality toward that end. Hope that helps.

I would just use cross domain canonical and look into the other issues with your website that have triggered Panda.

Again, thanks for the input from everyone. One of the things that I have noticed is that they did some link building to some specific categories on our website with specific anchor text and they ranked well at the beginning and the dropped off the face of the earth while some of the other categories that they didn't do link building on have continued to rank ok. Also, about a week ago we noticed our organic search results drop significantly. Could that be an identifier that Google has penalized our site due to those potentially spammy looking links?