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For the directories I think you need to go down the rewrite route.  This isn't probably functioning correctly but you get the principle.

RewriteCond %{THE_REQUEST} ^GET\ /category/
RewriteCond %{REQUEST_URI} !^/category/sub1/
RewriteCond %{REQUEST_URI} !^/category/sub2/
RewriteRule ^category/(.*) http://www.newdomain.com/category/$1 [L,R=301]

RewriteCond %{THE_REQUEST} ^GET\ /category/sub1
RewriteRule ^category/sub1(.*) http://www.newdomain.com/category/sub1/$1 [L,R=301]

RewriteCond %{THE_REQUEST} ^GET\ /category/sub2
RewriteRule ^category/sub2(.*) http://www.newdomain.com/category/sub2/$1 [L,R=301]

Have a look at this - https://support.google.com/webmasters/answer/66356?hl=en&rd=1

If you can't add the no-follow attribute to the ads then you need to use another mechanism as suggested:

• Redirecting the links to an intermediate page that is blocked from search engines with a robots.txt file

This is something you do your end.

No matter the source a paid for is a paid for and must not be "followed" so link equity could pass through.

If you cannot append the no-follow attribute to those links then something like this is your answer - https://yoast.com/cloak-affiliate-links/

Have you only recently updated your website, maybe the tool has not re-crawled yet?

What results do you get in Google for site:www.yourdomain.com?

What results do you get with https://moz.com/researchtools/crawl-test?

If you know it is backlinks then you should only need to cleanse your profile.  Manual - submit a reconsideration request; algorithmic - wait for an update.

If you do use a new domain you have no age, no authority and ranking will take time.  Being local you have to ensure every source that contains NAP is updated with the new domain as you cannot redirect if you suspect there is any infection within the existing profile.

All I am saying is that I don't know your domain or scenario, but just ditching to a new domain may give you more headaches than you envisage and should definitely not be a knee jerk reaction to a slow recovery.

Then as mentioned there is a trust thing with your visitors changing domain, especially if it is branded.  If you do go down that road I would get some business objective information out there as to why the change in name (on the site, social etc).

The simple answer is we cannot give you confident advice.  We don't know what the penalty/ies were, or if they are manual or algorithmic - do they tie up to any particular dates.  Then that is only the start of real identification.

Does the domain have authority, age and an element of good link profile?

Does the domain have on-site technical issues hampering recovery?

My take on the question is that if you do not know precisely what the problem is then starting a new domain there is every reason to suppose you may fall down the same hole again.  If you do know precisely the problem then fix it and wait, build out new content, create excellent links back to the site.

There are 2 distinct possible issues here

1. Search results are creating duplicate content

2. Search results are creating lots of thin content

You want to give the user every possibility of finding your products, but you don't want those search results indexed because you should already have your source product page indexed and aiming to rank well.  If not see last paragraph.

I slightly misread your post and took the URLs to be purely filtered. You should add disallow  /catalogsearch to your robots.txt and if any are indexed you can remove the directory in Webmaster Tools > Google Index > Remove URLs > Reason: Remove Directory.  This from Google - http://www.mattcutts.com/blog/search-results-in-search-results/

If your site has any other parameters not in that directory you can add them in Webmaster Tools > Crawl > URL Parameters > Let Googlebot Decide. Google will understand they are not the main URLs and treat them accordingly.

As a side issue with your search results it would be a good idea to analyse them in Analytics. You might find you have a trend, maybe something searched for or not the perfect match for the returned result, where you can create new more targeted content.

To back up the detail Wesley gave you, you can also add URL parameters in Google Webmaster Tools

https://support.google.com/webmasters/answer/1235687?hl=en

Everybody will direct you to the foot of the page to take a look at recommended companies - http://moz.com/community/recommended

Sponsorship is paid for so all those links should be no-follow

Having guest posts has, does and will still work if the primary purpose is to add value, be informative and be honestly relevant and not at all promotional - no keyword links spamming the content.  Personally I wouldn't actively promote guest posts on the site, rather let it happen naturally or through your networking.

Are you sure about the direct algorithmic penalty/penalties, do they tie in with the update release dates and was there significant drops in traffic to identify which update version/s caused the problems?

I've worked on sites where I would describe as suffering the residue of penalties from linking domains, along with masses of on-site technical issues.  Typically organic traffic has declined over a 1-2 year period.

I'm not suggesting you don't clean up your link profile, it is the right thing to do, but you want to be real sure what is causing the immediate problems.

I would install Fiddler and check the header response of your URLs. Otherwise screamingfrog is the way to go. Oleg might be right in that the developer might have set 302 redirects.  If you post the URL we could confirm for you.

In .htaccess if the redirect doesn't explicitly end with the R=301 directive, typically [R=301,L] then the default is a 302 temporary redirect which doesn't pass on link value.

Also for an accurate assessment of links I would use Open Site Explorer.

Are you sure it's just on Mac,have you tried on PC?   Do you have any other rules in include or perhaps a conflicting rule in exclude? Try running a single exclude rule, also on another small site to test.

Also from support if failing on all fronts:

• Mac version, please make sure you have the most up to date version of the OS which will update Java.
• Please uninstall, then reinstall the spider ensuring you are using the latest version and try again.

To be sure - http://www.youtube.com/watch?v=eOQ1DC0CBNs

your directories have duplication.  For example: http://www.titanappliancerepair.com/about-us.html and http://www.titanappliancerepair.com/about-us

You may also need   RewriteRule ^(.*).html$ /$1 [R=301**,**L]

It looks like you are redirecting any URL back to itself.

You want something like this which will remove index.html and enforce a trailing slash-

RewriteRule ^(.*)/index.html$ /$1/ [R=301,L]

Apart from reaching retirement age before your link is live in DMOZ and spending a fortune for Yahoo I wouldn't bother. I would only consider doing these as 'an also' activity.

I would focus on reaching out to high authority, highly relevant sites and seeing if there are ways you can work with each other to get great content on their sites with a natural link back to your domain.

If your rankings are still faltering you may need to go through your link profile with a fine tooth comb and remove anything that is not good quality or spammy.  Also ensure all your content is unique and you don't have multiple pages with thin content.

thanks. You've confirmed my thoughts on doing a thorough spring clean.

Thanks Chris.  Yes I agree no harm.  To be honest this is in the mix of getting Partial Matches: Unnatural links to your site—impacts links       "...so for this incident we are taking targeted action on the unnatural links..."

I don't totally subscribe to Google just removing link flow from the links they refer to and that's that nothing to worry about. So in the back of my mind i'm looking at a complete purge even if not technically applicable.

When you redirect A to B, B does not equal A, but rather inherits some of A's authority.

You will need to further develop the link profile of B with other mixed authority linking domains in order to improve it's own domain authority.  I wouldn't get hung up on pagerank, it's never current and only a contributing factor to overall domain authority.

I would use something like Open Site Explorer to gauge the overall domain authority and work from there.

Going back to your question the only way to retain that domain authority (in part pagerank) of A is to not 301 to B.  But I guess that if A has been bought out they want it to disappear into the main pot.

Looking at the link profile anchor text of a site i'm working on new links keep popping up in the reports with let's say very distasteful anchor text.  These links are obviously spam and link to old forum pages for the site that doesn't exist any more, so the majority seem to trigger the 404 page.

I understand that the 404 page (404 header response) does not flow any link power, or damage, but given the nature and volume of the sites linking to the "domain" would it be a good idea to completely disassociate and disavow these domains?