What tips do people have for implementing SEO strategies for large websites?
The problem with large sites is scalability. I am not talking about the hardware or software, but instead the human factor.
Pick an item for sale, let's go with wall clocks. If you have a small site which sells 50 wall clocks then each and every clock would probably have it's own page. Sure you can have category pages but there would probably be some level of intimacy offered. The site might have began with selling a single clock, then expanded with another clock every couple weeks over a period of two years.
Each clock page could tell a story. The page could talk about who designed the clock, the manufacturer, people who have bought the clock, rooms where the clock would look best in, some details about the clock's history, how the clock is the same or similar to the one from a movie scene, etc. Detailed images might be offered from various angles. There is a level of detail and personalization offered when a human being is involved with creating a web page and sharing a high quality experience. These pages offer a lot of value to visitors and therefore search engines.
On the other extreme, there are websites which carry tens of thousands of products. The site owner has never seen nor heard of the item being sold. The product is listed based on a feed, the page URL is clock12z43, the description feels more like reading the Supplement Facts label from a vitamin bottle, etc.
When the owner of the latter style of website asks "why doesn't my product page rank higher" I ask them in return how many hours are they willing to spend on the page building it with quality information to help it rank higher. The response is often none, and there is your roadblock. The explanation is the owner doesn't have the time or ability to spend an hour per page with 10k+ products. Often the e-commerce solution does not have the flexibility to accommodate reasonable changes either. The site is restricted by the gridlock of attempting to allow one person to manage 10k products which simply is not reasonable.
If I could offer one tip for managing a large site it would be treat each and every page as if it belonged to a small site. Each and every page should have a human review it, and it should look like a human was involved with it's development.
what is the best strategy for acquiring links
Again, that human interaction does wonders. If you build outstanding pages, allow user generated content and provide social integration, many links will come naturally. Whenever you feel your linking needs a boost, reach out to the community. For the clock example, there are many types of sites ranging from interior design to arts and crafts. Read their forums and become involved in their community. Participate in sincere, helpful discussions which do not necessarily involve your site. When a topic arises where you can smoothly share a link to one of your clocks, do so in a high quality (i.e. non-spammy) manner. This method is one of many techniques to build links.
should we target all deep pages or just the home page and category pages
A balance works best. All pages would benefit from links.