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You may want to read what MOZtrust is all about. However that would only be a starting point. Was the majority of traffic you lost within the "high quality" traffic realm? Or did you lose a proportional amount of conversions (whatever your site deems as someone taking an action you want after they come to the site)?
Mike's suggestion about understanding what the current value is for that site and all it's individual pages. If there had been significant value at one time and it's dropped off, you'll need to rebuild it all over again. Also, if you're buying old domains and replacing the content with all different content, you're essentially starting from scratch. Domain names by themselves won't provide enough value to make it worthwhile without all that new from-scratch work, and just using them for redirects is definitely not a quality SEO tactic in 2011.
Jonathan,
The "rule" used to be 100 links to a page based on Google having included that in their guidelines. They've since removed that numeric value without replacing it with another number. What I find in my large client sites where there's hundreds or thousands of products in a category is the pagination method. The key is to ensure to append each page's Title, URL and h1 with "Page X".
This is best simply because it helps ensure Google discovers all the products and properly credits them to the core category. By trying to force all of the products onto a single page, and using any method that hides most initially for usability, you introduce the possibility that not all those products will be discovered, no matter how much Google does a "good" job at discovering links inside CSS or JavaScript. In reality, their system is far from perfect, and with all that added code, the possibility exists that you cause crawl problems due to imperfect code.
and the good news is if you implement high quality content and focus on high quality links and social signals, you should eventually be able to overtake them. I've done it a number of times. As frustrating as it is to deal with, it can be dealt with.
If search bots can find the lowest level pages easily enough by other on-site links, then the only real question I would consider has to do with usability - can you present the site map in a way visually that is not overwhelming or confusing to site visitors, if those are included? Or alternately, by eliminating them, would someone using that site map be annoyed if those are not included?
The SEO value of such links on a site map page are ultimately insignificant at best.
I find some of the OpenSiteExplorer.org data that only comes with a Pro account, and the campaign monitoring in Pro Tools to be an invaluable part of my SEO audit and ongoing SEO toolset. Pro Q&A is a great place to come as often as you need to to ask questions and get some amazing feedback, answers, suggestions...
Daniel
If the site in question is indexed at Google under the https method rather than http, then yes, it should provide the same value as an http indexed site. a quick inurl: https; check just now brought back over 1.6 billion pages. Random checks of various keyword rankings for queries that contain a mix of http: and https: brought back a number of them where https: sites ranked higher than http: sites, including some with site links and multiple entries as well.
Also, I've got a couple financial institution clients who use https: and haven't seen any more difficulty ranking them through typical SEO methods. Which just reinforces that belief. If anyone here has had differing experiences I'd like to hear about it as well of course...
Actually it depends on the content and site intent.
Taking Tyler's suggestion further, If there are several products or services in each primary category then it could be:
domain.com/dodge/viper/roadster.html
domain.com/dodge/viper/sports-coup.html
Also, using "car" in the URL as Tyler suggests only makes sense if you are targeting the broad "car" related searches, or if you have categories such as "cars", "trucks" etc. And if you do, having domain.com/cars/ would be better than domain.com/car/
In any event, you also need to consider user experience - stuffing too many keywords in a URL can become ugly.
Do it right and you can get the additional benefit of Google including your URL structure in the SERP in a way that makes it look like breadcrumbs - replacing the URL shown.
Warrior Forum is sadly a self-perpetuating tank filled with sharks and shark-food. Mostly shark-food.
To add to Corey's response, I'll repeat what I just provided another question here on Pro Q&A. Sitemap.xml files can handle a maximum of 50,000 URLs, however I've seen them choke with as few as 10,000. Its important to run them through a tool like tools.pingdom.com to ensure they load within just a couple seconds.
Then submit them through Google/Bing webmaster systems and then see if they succeed in crawling all of them.
hahaha. The blind wanting to lead the blind. How many aspirants does it take to change an SEO lightbulb?
Jean,
The more important question is how relevant a directory or association site is to the market your trying to target? Inbound link profiles require you have links coming from sites and directories that have a variety of performance indicators, from relatively low up to as high as you can obtain.
If that association is quite appropriate to your site's purpose and intent, not only do you get the benefit of relevance relationships, you can also potentially get people clicking through to your site from your listing there. Highly relevant people. Which itself is both good for business and a strong signal to search engines that it's a valuable link, and your site is important.
Hi Mike
I'd definitely not pollute / dilute the focus of Y by keying in on X for that report. Sure, you can reference X in the report, or in linking to it, but that should be secondary only... Let this be an opportunity to build the strength of Y.
Hi Matt
I used to use Excel, but it can get out of hand over time. Personally, I prefer a project management system, such as Basecamp. You can set up milestone actions with a date of delivery, that becomes the date of record of completion. You can add to-do lists, files, notes, messages all tied to the milestone. Everything is then stored and can be archived for future retrieval.
It's not perfect, (no solution I've ever used is perfect), but it's much more organized and manageable than Excel, unless you are really skilled at Excel and have the patience and willingness to deal with it when it's got years worth of data.
It's really a process of experimenting over time to find out the method that results in the most URLs indexed that in turn brings the most relevant traffic. Personally I wouldn't have one for each category, yet without tests there's no conclusive reasoning either way.
I LOVE the notion of stars instead of "guru". But as I am now a lowly aspirant, it will be embarrassing if I only have like a half star or something. NO disrespect to aspirants. We were all lowly at one point. 
I have to agree with Daniel's first suggestion, and at the same time, caution that the 2nd suggestion could rapidly backfire because just one link from one blog is very insignificant in the long run. Multiply that by multiple doctors - how long do you think you'd be able to get away with the blog comment path before someone smelled a rat and reported it as spam? In the blink of an eye.
Local citations, local directories, and local listings and Yelp, CitySearch and the rest. Coupled with high quality unique content on each site where you seed location info into the on-site optimization.
If I understand your situation, you're talking about providing links to some other site from every page on your site. Is that correct? If so, yes, that's potentially a serious SEO problem. Too many links from one site to another can be considered link-stuffing. It's very possible that it's seen as a paid link.
Play with fire, get burned. Yes, you already know that. No, I don't think you personally should have to suffer through untold similar cliche's.
So here's the reality. Without cleaning up the profile, it's highly unlikely the site will ever recover. That leaves the only other reasonable option, which is the drastic one. Abandon the existing domain as far as SEO goes and start fresh with the clean domain.
That's potentially going to be the biggest challenge to get others to agree to, because those who have the guts to play with fire in a known dangerous environment typically have too big an ego to admit there isn't yet another quick and easy fix that instantly reaps big rewards on the scale that should never have been achieved previously in the first place.
However even Matt Cutts said this past week, that in worst case scenarios, people just may need to start with a new site. When Matt comes out and says that, you can be sure the potential for all hope to be gone on a now burned site to rebound is now lower than it ever was.
Lets go beyond the excellent input EGOL has provided for a moment.
How relevant are the articles you're dropping links in the comment area of to the site you're linking to? How relevant is the topic to the target topic? How much of your link building energy is focused on this as a link building tactic?
Comment links offer such little value even when all conditions are ideal that it's really not a prudent use of time and resources. At least not from an SEO best practices perspective.