@Ronyon - I second the @wesleysmits recommendation to prioritize products with key business value.
To address some of your points:
1. "Do I go with brand by brand? Do I go with products with good margin?".
- Go for the products that bring in the most profits for the company**.** Margins aren't exactly the key point. It's the real dollars coming in. If you have a product bringing in an incredible amount of money, your minor improvements will have magnified results. Example: Let's say the top product the site sells (out of 4k items) brings in $10k profit/mo. If you are able to improve sales on that single product (i.e. you ONLY do SEO + conversion improvements on that product), and you're able to boost sales by 50%, you're bringing $5k/mo more. That's $60k/yr. BY ONLY OPTIMIZING ONE PRODUCT.
- Go for products that are easiest to sell. If you have a products already bringing in a lot of organic search traffic, @egol is absolutely right. Improving the hook-i-ness of the title and creating the perfect description will have great impact. And it's EASY! If you have 100 visitors/day through organic search on just one product page, and you're able to improve the Click Through Rate by 10%, you've brought in 10 additional visits a day. Furthermore, if you can improve the product graphic or copy on the page, you might be able to boost conversion rates on that product. That's an additional sale every week or two. For an hour or two of work, not bad!
- It's OK to work on things one at a time. But you have to choose your battles. Make sure you're going to make an impact.
Here's another tip. Without knowing the big picture, it sounds like you need help w/ just the labor of the thing IF that's the case, then **make the case to the bean-counters that your work generates profits. If you had more help (hire another SEO), you'd be able to generate profits faster. Then you can also be a manager. **How?
- Create a before/after report of your work using Webmasters/Analytics.
- Take a snapshot of how the website is performing (Traffic per product page, CTR's, Conversion Rates, Bounce Rates, ranks for all the product pages)
- Do your SEO magic
- Go to your manager and say "Check out what I did. As a result of what I did in the past 3 months (for example), I'm bringing in $3.5k/mo extra for the next year. That justifies hiring a link-builder to help me out!"
This tip isn't just from me. There's a big tome of a book--The Art of SEO; co-authored by randfish--that spends Chapter 13 talking about "Building an in-house SEO team" (among other things). A great deal of that section talks about why it's so important to get buy-in from the organization.
SEO is a profit center. Management would love to make more money, faster. Give them a few good-looking charts, and get some help!