You've heard it before... the difference between an indie book which reads like a trad pubbed book and an indie book which reads like a vanity press heap of toad dung is all in how much effort you invest in doing the details.
The biggest priority is to have a good editor. I've found that having a team of Beta Readers as a follow-up is even better.
The next most important thing is to have a gorgeous cover which clearly communicates your book's genre and subgenre.
Finally, there is the issue of internal formatting. I admit, I gave no thought to this for the first couple of years. I couldn't afford to hire help, and I wasn't able to do it myself.
However, as eReaders have proliferated, screen quality has increased, and the tablet market has exploded, internally attractive books--with features like hyperlinked Tables of Contents--have become more important.
My formatting is now done by "Tech Guy." (He charges $50 an hour, if you're in need of a formatter.) He now has a blog, Unclogged, for those among you who are suitably nerdy. :) This dude has every eReader ever built, I swear, even those weird cheap brands that are so cheap, you've not only never heard of the brand, you've never even heard of the country where the brand is made. He recently posted about how to take screenshots of eReaders, and he used The Unfinished Song: Initiate, as his example. Check it out.