On June 30, 2012 MobileMe will be shutdown. HOWEVER, iWeb will still continue to work but without the following:
Features No Longer Available Once MobileMe is Discontinued or Using a Non-MMe Server:
◼ Password protection
◼ Blog and photo comments ➙ ➙ ➙ ➙ ➙ ➙ ➙ NOTE THIS
◼ Blog search
◼ Hit counter
◼ MobileMe Gallery
All of these features can be replaced with 3rd party options.
Since MMe is going away you could convert your iWeb blog over to WordPress complete with comments with this application by Rage: Convert Your iWeb Blog to a WordPress Blog | iWeb to WordPress for Mac OS X
I found that if I published my site to a folder on my hard drive and then uploaded with a 3rd party FTP client subscriptions to slideshows and the RSS feed were broken. If I published directly from iWeb to the FPT server those two features continued to work correctly.
There's another problem and that's with iWeb's popup slideshows. Once the MMe servers are no longer online the popup slideshow buttons will not display their images.
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However, Roddy McKay and I have figured out a way to modify existing sites with those slideshows and iWeb itself so that those images will display as expected once MobileMe servers are gone. How to is described in this tutorial: #26 - How to Modify iWeb So Popup Slideshows Will Work After MobileMe is Discontinued.
It's now confirmed that iWeb and iDVD have been discontinued by Apple. This is evidenced by the fact that new Macs are shipping with iLife 11 installed but without iWeb and iDVD.
This may be of interest to you: Life After MobileMe.
If you still want to use an iWeb blog and publish your site to GoDaddy then you can still enable comments by using something like http://www.intensedebate.com. It is free so try it and see.
You also have the alternative of ditching the iWeb blog and creating a new blog using WordPress and linking to it from your website. Rage have produced some software to allow you to transfer comments from an iWeb blog to WordPress. It is available on the App store.