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I do, I run a pretty large wiki (2400 articles, over 1000 users) and I can definitely vouch for it. Out of the box it uses canonical tags as well (for redirect pages), knows which pages it should index and which it shouldn't (edit & login pages for instance are noindexed) and Google can handle an out of the box install pretty well.

If needed you can even use one of the meta plugins to optimize your descriptions, titles and noindex/nofollow certain pages or even namespaces. (I wrote the AdvancedMeta plugin, but there's plenty of others).

First of all, you should try and visit the website using Google Webmaster Tools (with the 'visit as Google Bot' tool). If it shows a HTTP 301 redirect to the .com website, you'll know everything is working fine but your site just hasn't been indexed yet since the change.

If it shows anything else (probably the holding page), there might be something wrong with the way you redirect. You can try using one of the plugins to check for HTTP statuses (FireBug and Chrome's developer tools have basic features, FireFox's Live HTTP Headers plugin can show you more). See what is says the HTTP status is, and try and fix it.

Follow/nofollow tells Google whether to follow the links on that page, regardless of whether it should index it.

Follow is usually safer, because even if it doesn't add the page to Google's index it at least alows Google to follow the links and pass some PageRank around. If a login form is all there is, nofollow would be no problem either, but it can never hurt to have Google follow the links to other sections of your website.

The only time I use nofollow in combination with noindex if it's a page that links out a lot (like the almost obligatory 'Friends' or similar linking pages). Those pages I don't want to index AND don't want to pass pagerank through. Anything else: just follow.

Hmm, I meant to post my reply here instead as an answer but I can't seem to edit it anymore. Anyway, yes it's an HTML meta tag. See my other post.

It's an HTML tag and should be placed in your

Apparently, in 2007 Jamaluddin was involved in some kind of controversy concerning an HIV-positive monkey (http://ms.wikipedia.org/wiki/Khairy_Jamaluddin#Isu_beruk, I used Google Translate but it's not very clear).

Possibly a lot of pages just link to his wiki article using the work Beruk as past of the anchor text, or maybe even just as words surrounding the anchor text

If that were true, it would be possible to take out a competitor by setting up a link campaign to their website. I do not believe Google would allow such a thing to happen, so while I'm not 100% certain I think it's safe to say bad inlinks will not harm you. I must admit though, the two observations (dropping search engine traffic and a huge amount of bad inlinks) do seem rather coincidental, especially taking in account that the Panda update hit in February.