Last week at SMX Advanced, Maile Ohye of Google warned SMX attendees of using the noscript tag on their web site. She said something like it is an "automatic" issue of some sorts.
I decided to dig deeper and ask John Mueller more about what is meant by "automated." So I asked John in a Google Webmaster Hangout on Google+ and you can listen to it at 49 minutes and 10 seconds in.
John implied that there is no "penalty" for using the tag but spammers have historically tried to stuff and spam in the noscript tag. So Google simply ignores or does not trust content within the noscript tag. So if you have important content and links, make sure that you just don't have it in your noscript tag.
John didn't go as far to say you shouldn't use the noscript tag at all, he said you can but don't put important content in there.
Here is the video:
Back in 2010, John gave similar advice on the noscript tag.
Forum discussion at Google+.