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Totally depends on the niche I am afraid. however for small businesses, I always advise takingthe manual route - although old, the strategies here still work:
http://www.seomoz.org/blog/small-business-link-building-part-a-analysing-opportunities
http://www.seomoz.org/ugc/small-business-link-building-part-b-grabbing-the-bull-by-the-horns
Could you add a screenshot - I may be being thick - but I still dont get where you areseeing info - a screenshot may help a bit 
SEM Rush is a pretty good tool outside the SEOmoz and google toolset...
Alternatively, run a PPC camaign for a day or two on the full set - will probably give you the most accurate data, instantly...
If you are using WP then its fairly easy, as you get inbound pings.
However, for non blogging platforms, its usually a good idea to set up a referring sites filter in your analytics, you should be able to spot referrals from sites that link to you, even if it is just a single referral... Doesnt cat them all, but does catch a fair few...
Are you syndicating the content for link building? Or are scrapers just pulling in your content?
On the note of tags and archives, in most cases this is best practice anyway. However it seems you may have been hit with the content udate, and as Shailendra suggests, you may want to get webmaster support people to look into your site.
Without a full analysis it is difficult to say what else is affecting your site.
To start with if the forum ISNT indexed, get the URLS changed, and try and get all the titles customosed so they arent generic across every thread.
I suggest a subdomain for forums, as you point out, it is seen as a separate site. you can always flow strenght from the forum into the main TLD by cross linking, which I think is much better to do, however some may disagree with this.
If I were in your position, I would prefer to release section by section - a massive blast of content would be more of a flag then a slow release - this is my personal opinion.
Re threads - I would follow/noindex all threads tht arent on the first page of the post - that way, the juice follows and gets crawled. Adding relcanon to those may also help preserve the strength...
Sorry - I had to giggle when I first read your question
1. Google has made changes to algo that is finding a number of these sites , especially ones with dupe content
2. They are in the process of downgrading the value of exact match domains.
My advice? If you are adamant n getting these sites back up, take one - customise the template, make sure its not linked to or or linking to any of your others - rewrite the content and make it unique, and then send in a reinclusion request to google, outlining what you did and WHY you did it...
Was this before or AFTER the Panda Update? If after, you may have been hit by G's new algo which targets sites they deem to be of low quality.
As Richard says, good job on the use of video sitemaps - this is one of the most probable reasons fro seeing the difference that you are
Yes and No. These are what I would call Sammy links - you are basically using a umber of forums etc to get backlinks, in qantity from the same provider. Soon enough, most of these forums would be loaded with so many link cheats that the whole value of the forum would die out. You may get a short term boost, but I would advise against it.
Some of these link profiles are what we call "dirty" i.e more likely to get penalised.
I came in to add link to my post http://explicitly.me/manipulating-google-suggest-results-–-an-alternative-theory but seems coule of people have already done that Thanks guys!
My honest advice? Use the traffic esti,ator only as a guideline. Google KW tool is FUBAR in many instances - for example, one search term it promises 10,000 searches a month, which I rank 1 for, only gets a portion of that if I look at the impressions i webmaster tools (another stupid tool) and only a fraction of the traffic you would expect, nowhere near if the data was correct.