Some Google Reader Strategies
Tagging
The first strategy that will make using Reader a beneficial experience for you is using tags to organize your subscriptions. My approach is to start by grouping and categorizing my subscriptions so that I can read through the latest feeds I've received within a common context. For example, I have about 24 subscriptions that are all tagged as "technology." These include various blogs that report on subjects like new software and hardware, the ethics of technology, tech R&D, and some company-specific news. But because many of these feeds may deliver the same stories to my Reader account, viewing them in chronological order and grouped by tag helps me to skim through them faster and isolate one article to represent a story reported by many subscriptions. I use about 14 different tags to categorize all my subscriptions and have little bleed from one category to another. When you use tags in this way, they will appear like folders (
) that organize your subscription list on the left side of your Reader account screen. You can actually drag and drop subscriptions from one folder to another to re-categorize them. However, you can also assign a tag to individual articles rather than to entire subscriptions. You might find this method helpful for researching purposes or just for when a particular article merits its own unique tag. When you use a tag in this way, it will appear with a "tag" icon (
) at the bottom of your subscription list.
Shortcuts
I also prefer to go through my subscriptions using the expanded view, rather than the list view. The expanded view lets me see the entire article so that I can skim through it, rather than using just the title and a snippet to decide if I want to read it, discard it, or share it with a friend. Using the Reader keyboard shortcuts is really helpful here; you can hit "j" or "k" to skip to the next or previous articles rather than having to scroll using your mouse, "m" to mark an article as "read," or "shift + m" to mark all articles as "read." I've never been a strong user of keyboard shortcuts until I started using Reader and realized just how much time using them actually saved! Believe me when I say that the more subscriptions you have, the more important it will be to you to use time-saving methods like keyboard shortcuts.

Starring
Starring is a Google favorite. If you use Gmail, you've probably starred (
) an email before- for a variety of different reasons. The neat thing about starring is that it's a feature that you can use for whatever purpose you choose, though it's probably best suited for drawing attention to something, as if to say, "this is important," or "follow up on this." Eric and I decided to start using the star in Reader to indicate articles that we read in full after we realized that Reader really has no way to distinguish between whether you skimmed an article or actually read it. As long as you scroll through an article and reach the next one, Reader will mark it as "read," even though you may not have actually read a single word. By starring the articles I actually read thoroughly, I can look at a list of my starred items in the Reader trends view (more on trends on the next page) to see which subscriptions are most important to me overall.

Update (hat tip to Eric): Copyblogger has a good article titled "How to Read," which discusses the 4 levels of reading from Mortimer Adler's How to Read a Book (in my library). Good stuff.
I love the conclusion:
Thanks for that primer. It still seems like it can absorb a lot of time to set up the subscriptions in the first place but at least you give a practical way to organise and sift through the overwhelming amount of information.