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I assume that the Kindle will most likely be available in the UK this year, and if you buy the US version now its wireless connection won't work in Europe.
On the iLiad, you would annotate PDFs using handwriting via the stylus. I don't think you can annotate MOBI files. You can merge the annotations into an updated PDF, and they can also be converted to typed text on a Windows PC.
On the Kindle all you have is TXT and AZW (MOBI) files, with other formats converted to AZW off-line, and you annotate them using the keyboard (which is ok for typing short messages). You can also "clip" an entire page of an e-book to the "My Clippings" TXT file, which also contains a copy of your notes. The number of clippings may be limited by the publisher of the e-book though.
I don't annotate myself, but I am impressed by the capability Amazon has squeezed out of the keyboard. Another area where the Kindle is ahead of the pack is all-documents search, which (according to the manual) includes your annotations. It will find all occurrences of the search term in all your e-books on the Kindle.
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