Thanks for the heads up about the links. They've been fixed.

A company having multiple websites may or may not be spammy. Obviously, if the multiple websites solely there to target specific keywords (e.g. target-keyword1.com, target-keyword2.com, etc.) then that's a spam issue, but it's not really a penguin spam issue. Penguin is about spammy links. So, if each of those sites had legit links, they wouldn't run afoul of Penguin. Panda, the Exact Match Domain update, and some others (including Googler manually reviewing sites) are more apt to handle that kind of spam. The links between the two would probably get devalued by Penguin, though. So, either Penguin missed the sites you're seeing (which is entirely possible) or the links between the two sites isn't the cause of their high rankings.

As for a company having two pages of their one site in the top rankings, that's usually taken care of by Google's main algorithm. They don't like having two listings from 1 site in the top ten. That said, it really depends on how competitive a keyword/niche we're talking about. Keywords with few results and niches with few compeitors will often still have multiple results in the top ten for a single site. Matt Cutts did say they are working on that, though. So, you should see this less and less in the coming months.

Lastly, in regards to whether Penguin is being rolled out in stages, I don't think so. There's been no indication that Google is doing that, but they have said there will be more updates coming out in the future. My guess is that we'll get a few refreshes over the rest of the year and at some point they will release Penguin 3.0. They may also just integrate Penguin into the main algorithm like they did with Panda.

I don’t see where this update in Google has helped particular searches and was wondering if they are rolling it out over time. Some issues I see – on the first page of SERP – same company listed twice with two different web pages under the same domain. Or companies that have two different domains in the same space exchanging links to push their two sites to the top. While this may be borderline okay, it is unethical – especially in the church market.