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There are  possible approaches around this that I can see.  The first might be to get rid of your new web site from the web after which absolutely noindex your antique site (blocking through robots.Txt may not do it - I've attempted.) You can then use the URL of office chair elimination tool to do away with the old web site absolutely from the index.

Hopefully in the next couple of weeks I should have some information on my tests on ways to safely redirect penalized sites.  I'm reluctant to give advice until then.  On one hand, you could say that because your penalty is removed you could just go ahead and institute a 301 redirect now.  However, I would not recommend this.  The reason for that is that even though you've had a manual penalty removed, there is still a possibility that there are links out there that could harm your sites in the eyes of Penguin.  I would not want to redirect any of the bad links to the new site.

When I do have my tests done I'll post here.  In the meantime, if others have ideas, it would be awesome to hear of their experiences.

Hi! You do need to type in the nickname of the user when you click Private Message this User. I know it's not very intuitive, but you'll want to type in MarieHaynes to send a message to Marie.

Sorry I haven't been able to respond again by email.  I'm at Mozcon right now and typing from the airport.  It's been a crazy, busy, fun week.    I'll respond here though rather than by email as it may help others.

I am fairly certain that the problem here is all because your new site has the exact same content on the homepage as the old site does.  As the old page was the one that Google first saw with that content, the new page is automatically being canonicalized to the old (even though you have the correct canonical on the new.)  What I think is happening is that when you noindexed the old page, because of the invisible canonical, the new page got noindexed as well.

I remember Matt Cutts or John Mueller saying something before about how you should not point a rel canonical at a noindexed page because it can confuse Google.  You didn't point the canonical there, but Google has probably assigned it because it was a duplication of the old page.

If this is true, then here are the possible solutions that I can think of:

-Create new content on the new page (which you have already done.)  I would then use fetch as googlebot to get google to refetch that page.  If I'm right, it should be back in the index quickly.

-If that doesn't work, consider removing the noindex from the old page until you see the new page pop back in the index.  You'll likely also have to remove any robots.txt block of the old page so that Google can see that you want it indexed again.  Then, once you see the new page is back in the index, and that the new content on your new page is in the cache, you can go back and reapply the noindex on the old page.

Hopefully that's not too confusing.

I want to hold off for now on answering your question about how to redirect users from the old site to the new without passing along a penalty.  The reason is that no one knows for sure which methods work safely to do this and be guaranteed that you're not passing along link juice from unnatural links.  Does link equity travel through a meta refresh?  I'm guessing no, but I can't say for sure.  I want to say that you can 301 the old page to an intermediary page that is blocked by robots.txt and then redirect it back to the new page, but I have to do some more tests before I am comfortable saying this with certainty.  There are other solutions that may work as well.

I currently have some tests going on that will help me determine which method is safe for redirecting without passing on a penalty and I'll post something to my site once I've got the tests complete enough.

Perhaps someone with more experience in doing this type of thing will see your question and respond too...I'm open to suggestions!

Interesting.  I see you've reached me via my contact form.  I've flagged your question so that the Moz staff can look into it and see if there is an issue with private messaging.

This is really odd.  I can't see any real reason for Google to noindex your current site.

I wouldn't remove the tag from the old site.  It doesn't make sense that this would affect your new site.

Would you be interested in sharing your url with me?  This case really interests me and I'd love to help you sort it out.  Feel free to contact me via my Moz profile.  I'm currently at MozCon right now, so I might not be able to reply right away but I'd like to sort this out as it is an odd case.

Hmmmm....that's odd that your homepage is out of the index.  Some things to check:

-are you absolutely sure that the homepage is gone?  If you do a site:search does the homepage exist anywhere?

-Check you haven't accidentally blocked your home page with robots.txt or accidentally noindexed it instead of the old site.

-Are you absolutely sure you haven't done a url removal for the new site by mistake?

You could also ask Google to fetch that page via webmaster tools and that may help it reappear quicker.

I think that the main problem here is that no one knows for sure what kind of things can pass on a link related penalty.  So, from what I know of your situation, here's what I'd say:

-Change your home page content on the new page so that it is significantly different from the old page.  The reason for this is that Google seems to be able to recognize that the links that used to point to that exact content should now be pointing at the new page.  If the new page changes then the "via this intermediate link" should really go.

-Remove any canonical tags that point from the old site to the new

-Most likely having a nofollowed link saying "we've moved" and pointing at the new site would be safe.  I can't say that 100% for sure though.

-I actually would not block the old site by robots.txt UNTIL you have noindexed the page and have seen that it is no longer in the Google results.  So, add to the page and then use the url removal tool found in Webmaster Tools to ask Google to completely remove that page from the index and the cache.  (You'll get a choice of just the index or index+cache - Choose the latter.)  That should result in the page leaving the index within 24 hours.  You'll know if it is in the index if you do a site:yoursite.com search and see "no results".  Once that has happened, then you can add the robots.txt directive to disallow the home page (or really, all of the site).

The reason why you want to do it in this order is that if you add the robots.txt block right now then Google won't be able to recrawl the page to recognize that you've changed the canonical and the noindex status.

I did this for one other site and the "via this intermediate" link notices disappeared in about 2 weeks.

I would love if you could update this thread with what happens.

I think this is the right time to use "nofollow, noindex" what i will do is change the content of the page where your visitors visits the most and want to redirect to the new one. Change it contents and warn visitors that you will be redirected to a new site and then do a meta refresh (do not use domain forwarding as some hosting converts it to 301, do not use canonical as well) meta refresh it for 5 seconds or more enough for your users to read the content just not shorter than 5 seconds (just to be safe) do not place a link on the content (just to be safe again) just remember to use "nofollow, noindex" on all the pages of your old site and disallow on your robots.txt

hope this helps

Seriously why complicate things? The problem was the old site and you know it thats the very reason why you created a new site. Just like MarieHaynes said "It sounds like a complicated situation though so I don't think we can give you a complete answer without having a deeper look at your site" maybe wait for few weeks and let google find your site again and if you have corrected your site, google will eventually correct its data too.

Best of luck.

If you've removed the canonical tag AND there are no duplicate pages on the new site from the old site then I'd think that the via this intermediate link messages should go within 2-3 weeks.

It sounds like a complicated situation though so I don't think we can give you a complete answer without having a deeper look at your site which is something that probably goes beyond the scope of a forum question.

Regarding your manual penalty most likely it has expired.  More info here: http://searchenginewatch.com/article/2345875/Did-Your-Manual-Penalty-Disappear-It-Probably-Expired

Awesome tip about transferring with the same content here. Completely noindexing the old site sounds like a good option. I'm going to have to keep this trick under my hat for a rainy day, thanks!

If your content is the same on the new site as the old then believe it or not, you don't even need a canonical tag for Google to recognize that this is the same site and apply your old links to your new site.

Here's more info on this: http://www.seroundtable.com/google-penalty-site-move-18163.html

There are two possible ways around this that I can see.  The first would be to remove your new site from the web and then completely noindex your old site (blocking by robots.txt won't do it - I've tried.) You can then use the url removal tool to remove the old site completely from the index.  It's important that the noindex tags are in place otherwise they may pop up again at some point.  Once the old site is completely removed then you can add the new site.  I've done this with another site and the "via this intermediate" links have not come back.

If you have pages on your old site that have good links and you want to 301 them to the new site you could keep them live, noindex the page and then do a redirect that goes through an intermediate page that's blocked by robots.txt.  BUT, know that this passes all link juice to the page. If there are bad links then there's nothing you can do to just pass the good juice along.  I haven't done this and it's complicated.  There's more information on that here: http://www.hiswebmarketing.com/can-you-recover-from-penguin-by-301-redirecting-your-homepage/.

Ideally the best way to ensure that you are not causing Google to see a canonical is to create brand new pages with new content.

Moving a penalized site is tricky!

If you're trying to transfer the good SEO juice, but leave the manual action on the old site, that might not be possible. Google has been cracking down on that, and if you try to move over the good stuff, the bad will follow.

It looks like you have two options:

1. You can 301 the old site, disavow all the bad links, and hope for the best. This way you aren't completely starting from scratch, but the amount of ranks you'll recover won't be clear until a few weeks after you do complete this strategy. Different sites have different results doing this.  It depends on the penalty, how well you clean up the links, etc.

2. Start from scratch. New content, new domain, new everything, so there's no relation to the penalized site. This might be what you want to do if the manual action is severe. It'll take a bit more analysis than seeing one keyword drop to know the extent of the penalty you're experiencing.

History is showing us that canonical tags are very powerful, and do pass pagerank. Canonical tags and 301 redirects pass roughly the same authority, so even if your physical links are nofollow, those canonical tags are still being interpreted by bots as a link-like entity.

So, by cananocalizing your old domain to your new one, you effectively moved all those links to your new domain, just like they would have with a 301.