I figured it's time to clear the air about identifying the Google "sandbox" penalty and comparing/contrasting it to other effects that can "appear" sandboxy. Here are the steps to take to determine if you're in Google's sandbox:

1. Do a site: command at Google (example)
   If all of your site's pages have been crawled and none are in supplementary results or have the only the URL listed, you can proceed to step 2 (otherwise you'll need to look at other factors - dup content, possible spam penalties, devaluation, technical issues, etc.). See Todd's post about these issues.
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2. Check your rankings for several of the most targeted phrases you're going after at the following places:
1. Yahoo!
2. MSN
3. AskJeeves (or Teoma)
4. Google's allinanchor search (example)
5. Google's allintext search (example)
6. Google's allinurl search (example)
7. Google with -asdf x 20 (example)
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3. Now compare the rankings from Google against all the rest. If you see, consistently, that you rank in the top 5-10 positions at all of those locations for a variety of targeted keywords, yet your rankings at Google for all of these is in positions 60-300, you're most likely "boxed."
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4. The List:
1. You cannot be "boxed" for just one term, that's something different (I'm working on IDing it now).
2. You cannot be "boxed" for only certain pages, also something different.
3. You cannot be thrown into the "box" unless you change domains (301), start a new site, or change all your registry info (i.e. sell the site). At least, we've never seen an example of it (and believe me when I say I get to see a lot of sandboxed sites).
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5. Caveat - If you rank around position #7-12 at Yahoo! and MSN and in the Google "allin" searches, and rank in the 50s or 60s at Google, this still may not be sandbox - Google is CRAZY-SUPER-PICKY about the quality of your links, so before you jump to assumptions in a position like this, I'd seek to get yourself some very high quality links and make sure you're ranking top 2-3 at Yahoo!, MSN, and the allins before jumping to conclusions.
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6. AskJeeves is a great litmus test. Because Ask is so slow about updating rankings, recognizing links, etc. if you are rocking at Ask for competitive terms and stuck in 3 digits at Google, that's a very good sandbox indication (taken in concert with the other data). Ask is also very picky about which links it counts (for most segments), so you can be relatively proud of yourself if you can kick butt with the butler.

I hope this checklist is educational for those seeking to determine if they've been "boxed" - comments are open if you disagree or think there are other criteria to consider.