I was astounded to see that Matt Cutts (in this session) advised people that blocking Archive.Org through robots.txt is a major spam signal. I've explained why I disagree with him on Best SEO Blog in a post titled "Why Some Sites MUST Block Archive.Org". Link not included because the spam filter will hold it for moderation.

There ARE legitimate reasons to block Archive.Org and SEOs should listen to why their clients want to block the archive before assuming they do anything wrong.

*I* block archive.org on some sites and have not suffered any penalties.

Same here. Why blocking archives.org is a red flag ? I don't spam, but I could totally desire to stay out of archives.org for other reasons.
For instance, I don't want to show off how ugly was my site in its first stages.
Maybe I completely changed the topic of the site; thus, don't want people to check what the site was in a previous life.
Google spam team is going way to far about some parameters that have nothing to do with Google. This one is a prime example

So Matt Tweeted me about this, and I have updated two blog posts (and ReTweeted) his clarification. He said to me: "if I'm already investigating a site which is spammy-looking and appears off-topic/expired, then IA block is very noticeable."

Fair enough, in my book (and I had already deduced as much). I just fear that people in the SEO community will start telling folks to NOT block IA_ARCHIVER when many sites already do this for legitimate reasons.

Matt is NOT saying that will get you flagged as a spammer (by itself).