An interesting post in webmasterworld.com describes how sites were dropped from google's index, whether it is because of a penalty or because of google's own problem, this checklist describes wel,

One of the most common themes of posting here in WW starts something like:
"Last night, my site disappeared..."
"Losing" a site can be a painful and
frustrating experience. To help ease the pain, perhaps a starting list of
potential issues might help. I'll probably miss more than I'm catching with this
list, but at least it's a start.
Do a site search at the SE in question to
determine if all of some of your pages are gone. Some think that their site has
vanished, when in fact an algo update or tweak has occured causing their pages
to drop. Or, individual pages have been filtered or penalized, but not entire
sites:
If *all* of your pages are gone (search on URL's to check that), then
perhaps: • your server was down at an inopportune time. • you have a robots.txt
problem. • you've been removed from the index based on a perception of bad
behavior (not good).
If only some pages are gone, or if your pages have
simply dropped badly in the SERP's, then perhaps: • you have some other
technical issue not noted above (e.g., badly executed redirects), • the algo
changed, • you've done something recently that the SE did not like, or, • the
algo changed and something that was previously "OK" is now being filtered or
penalized.
Here are some specific things to look at:
Start with the
basics: Was your server down recently? Server failure is always a good item to
check off your list when searching for problems. No need to start remaking your
site if all that happened was a temporary problem.
Are you using a
robots.txt file, and if so, has it changed. , Is the syntax correct? There are a
variety of potential problems that can be caused by improper code in robots.txt
files, or placement of the robots.txt file in the wrong location. Search WW on
this topic if you're not sure what you're doing. Use the WW Server Header
Checker. At worst, a robots.txt file can tell a SE to go away, and you really
don't want that. ;-)
Have you more aggressively optimized recently? Internal
changes that can lead to potential problems include: • More aggressive kw
optimization, e.g., changes to Titles, META's, tags, placement and
density of kw's, etc. • Link structure changes, and especially link text
changes. Updates to link text or structure, if done for optimization reasons,
can push a site into filter/penalty territory. Look in particular for overuse of
kw's.
Have you added redirects? The SE's *can* sometimes become confused by
redirects. Assuming that the changes are intended to be permanent, use 301's,
not 302's. Be especially careful about large scale changes. If done properly,
redircts are important tools. Done without proper knowledge, they can lead to
short term pain, often on the order of 1-6 months.
webmasterworld.com/forum3/8706.htm
Do you have a significant number of
interlinking sites? If ever there was a strategy that might be summed up as:
"Here today, gone tomorrow..." interlinking is it. You can succeed with this
strategy. But if you add too many sites or links to the mini-net you're
creating, or interlink too aggressively, it can catch up to you. Penalties can
range from soft filters to complete manual removal in rare cases. Even with no
recent changes to your sites, the SE algo's can change, making something that
squeeked by yesterday illegal today. webmasterworld.com/forum3/4618.htm
Are
you linking to sites in "bad" neighborhoods? If ever there was a strategy that
might be summed up as: "Gone today..." linking to "bad" sites is it. If you
think that you might be linking to the dark-side, lose that link instantly, if
not sooner.
webmasterworld.com/forum3/8053.htm
Could you be suffering from a
duplicate content penalty? Some practices or occurances that can cause problems
in this regard include: • Use of a single, site-wide template • Use of one
template across multiple sites • Competitors stealing or mirroring your content
• Redirects from an old domain to a new one • Over reliance on robots.txt files
to exclude bots from content areas you don't want exposed. WebmasterWorld
Thread: webmasterworld.com/forum3/22494.htm
Are you cloaking? Some cloak merely to deliver "accurate" pictures of
sites/pages to the SE's. Examples of this are sites with lots of graphics and
little text. But if you're a mainly text based site that is delivering one set
of content to the SE's while users are seeing something
less...umm...optimized...then there's always the risk that you've been caught.
Are you using AdWords? This is pure speculation on the part of some seniors
here, but some do seem to firmly believe that if you place highly with an
Adwords listing, it might actually hurt your position in the SERP's. Don't shoot
me. I'm just the messenger.
IF OTOH, the only issue is that you're not as
high in the rankings as you'd like, then a better place to start would be
Brett's 26 Steps to 15K a Day.

Source: http://www.webmasterworld.com/forum5/4584.htm

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