Kindle Club

I think the Amazon Kindle DX should suit best of your need, and it is also the best e-book reader right now in the market. Yes, you can only buy books in Kindle version from Amazon. However, the best thing is that the Kindle DX supports PDF natively, so you can buy any books in PDF format and they can be read well on the Kindle DX.

Read the fifth paragraph of the review here about bookmarking function of the Kindle DX:

Hope it helps.

The Amazon Kindle and the Sony Reader are the two best and most popular e-book readers on the market, and among these two the Amazon Kindle is the best. However, currently there is not any profession e-book reader which comes with a color screen…

Among all the ebook readers, the Amazon Kindle is the best on handling PDF files. You can read these reviews to know more about it:

If the Kindle DX still cannot match what you need, I think you’ll need to wait for some newer e-book reader with more advanced technology to come out…

Unfortunately there are no ebook readers having colour screen. I think the best one that suits your need is the Kindle DX. Even though the Kindle is closely linked to the Kindle store, there are over 320,000 Kindle books available and it is kept on increasing. It is largest ebook resource among all the e-book readers right now.

There is Sony Reader but Sony provides even less choice on books compared to the Kindle, it will be more difficult to find books for the Sony Reader and price of books on Sony Reader is more expensive.

I suggest you to read this review by an actual Kindle DX owner. It mentions about journal handling in the middle of the review:

Unfortunately, none of the current e-ink readers are really good for PDFs.

The Kindle DX doesn’t have any search or annotation functions for PDFs, so it won’t work for that.

The Sony PRS-700 has a smaller screen, but does allow annotations; it’s mostly being replaced by the soon-to-be-relased Sony PRS-600. (The 700 isn’t being made anymore, although several stores still have them.) But a lot of people think the screen on the 700 is blurry; it’s got a built-in light around the edges that make it thicker than is comfortable to read. (The 600 doesn’t have the light.)

The iRex 1000DS has annotations, and possibly wifi–but it’s *really* expensive, and older tech so it only has 4 levels of grayscale. (No e-ink readers have color yet.)

For annotations of PDFs, you’re probably best off with a low-end netbook, which are about as cheap as the dedicated e-ink readers. They have color, allow all sorts of useful software, and have wifi–the drawbacks are that they have the larger screen, and shorter battery life than dedicated ebook devices. But some of them are quite small and light.