This is the best pdf document I have found for the Holy Quran for the Kobo, Kindle and Nook. I will post screen shots from Kobo Touch and hope that some one who has downloaded this on their Kindle and Nook can share their experiences. I have modified the Table of Contents which is essential for a good ereading experience. The Table of Contents has a few screens by which the bookmarks are organized. These are as follows
1. Five Surah & 4 Qul
2. Juzz Number
3. Surah Index (Alphabtically)
With these bookmarks above you can navigate easily to any Surah or Juzz. This is the link to download this eQuran
I will post screenshots of how this looks on my kobo.
Update April 27, 2012: I am attaching screenshots of Quran in my Kobo Touch (low resolution). If you have screenshots to share from your devices please post in comments and I will move them in main body of this article.