I have a site that does well with Adsense from all organic traffic in a fairly competitive niche. I really like the theme I use and it converts very well. If I start a new site with a completely different niche and all completely different content but I use the same layout and theme, will I be penalized in the SERPS? I don't want to bring down my good site. I heard dupe content referred only to written content. Do SE's penalize for the same customized theme though as well?
No, you shouldn't have a problem. Just don't cross link them until any duplicate content issue is resolved. Remember, the template is "common code" and that is considered content. Will Google see the "common code" as duplicate content?
Why would you be? You need to understand what's going on with duplicate content. As an information retrieval system, search engines don't want to clutter up their database with repeats of the same information so duplicates get filtered out. This helps the user too as they don't get the same article appearing 100 times when they search for something. It's not a penalty, it's simply removing redundant information because it makes sense to. Given that it's the content being duplicated that is the problem, you can work out that the theme/layout that you use on a site doesn't matter. In addition to it not making sense to penalise for replicating a layout, there's plenty of evidence out there that shows this doesn't happen. Look at all the wordpress blogs that use the same free themes for example.