+5  A: 

you can always use robot.txt on backup.* site to disallow google to index it.

More info here: link text

Zepplock
Additionally, you may want to do a 301 permanent redirect from your backup site to your main site for unrecognized IP blocks. This ought to cause Google to remove the entries for the old backup site.
Bob Aman
+7  A: 

You should probably put a robots.txt file in your backup site and tell robots not to crawl it at all. Google will obey the restrictions though not all crawlers will. You might want to check out the options available to you at Google's WebMaster Central. Ask Google and see if they will remove the errant links for you from their data.

tvanfosson
+4  A: 

Are the URL formats consistent enough between the backup and current site that you could redirect a given page on the backup site to its equivalent on the current one? If so you could do so, having the backup site send 301 Permanent Redirects to each of the equivalent pages on the site you actually want indexed. The redirecting pages should drop out of the index (after how much time, I do not know).

If not, definitely look into robots.txt as Zepplock mentioned. After setting the robots.txt you can expedite removal from Google's index with their Webmaster Tools

Ben
Throught Webmaster Tools, you can control what they index pretty well. This should give you the power you need to get it un-indexed.
Chris Missal
A: 

Also you can make a rule in your scripts to redirect with header 301 each page to new one

Novinite
A: 

Robots.txt is a good suggestion but...Google doesn't always listen. Yea, that's right, they don't always listen.

So, disallow all spiders but....also put this in your header

<meta name="robots" content="noindex, nofollow, noarchive" />

It's better to be safe than sorry. Meta commands are like yelling at Google "I DONT WANT YOU TO DO THIS TO THIS PAGE". :)

Do both, save yourself some pain. :)

Monkey
Oh, Google will keep your files. Even if you delete them from the internet. That's why you need the 'noarchive' tag.And 301 all the backup files to the original files. This will solve the PR question and storage question.
Monkey