My iBooks is having trouble loading books since I have a few hundred books on it.  Bluefire and eBookS Reader both have let me down when I have tried to download certain books to them.  Both these readers have refused to open when I have downloaded certain books.  My guess is that they were books with DRM's still showing somewhere.   The only solution was to delete the apps and all of the books.    Apabi will not turn pages for me on the iPad but will on the iPod.  Love that it will do collections though but not good when it will not turn pages.  Mes Libres won't go past page one on some books but the books work fine on other readers.  I could go on and on about my trials with ereaders.  I am somewhat of a speed reader and want to keep the books I have bought and the ones that were free.  I do re-read a lot of books.  Right now I am frustrated and want to be reading not fighting with ereader apps.

Edited to add I have Apabi working now and it seems to be doing well.  It may just be my second favourite reader as I can organize it into collections. 

Does anyone have recommendations as to which is best?  I might add that neither of my devices is jail broken and I have no interest in doing that. 

I have iBooks to read iTunes books.  Most of the time I use Stanza to read epubs and Kindle to read mobi books.  For reading txt books, try Share Reader HD (got it when it was free and it can be used to read html, pdf, epub, doc, txt).  For html books, try USB Sharp Pro (also has music player that supports lyric search).  Kobo, Ouiivo (for epubs) and DocStorm (pdf) are also alright.
I like to have a few readers in my iPad (in case any don't work after an iOS or app update, I can still use another).

P/s BTW, my device is not jailbroken too.  Plenty of free apps giveaways if you watch out for it, so there's no need to jailbreak.  Stanza and Kindle is free and the best alternative to iBooks.  (Kobo & Ouiivo is also free, but I removed them because there's nothing special about the apps).

Edit : March 22, 2013
There's a free app for iPad (Documents by Readdle) with Dropbox, Box.net and Google Drive support.  The app also allows you to set password (your 'sensitive' docs/ebooks/music-room-tell-us-what-you-listen-too-15700/pics are for your eyes only) which iBooks doesn't have.  I'm using this more as a pdf reader because it 'remembers' (auto-bookmark?) the page you stop reading.  It also allows viewing of countless other files, including office documents.  A must-have on your iPad.

Wow, thank you for sharing.  I am really impressed with this book reader.  It has many different features, like being able to read the metadata/description of the book if there is one.  iBooks doesn't have that feature.  There is a much greater selection of background and text colors to choose from, you can choose night and day mode.  I love the feature of being able to share this book so easily directly from the app. 

The one drawback is that I do not see a feature for sorting books into collections like iBooks has.  Sure you can sort authors but that isn't not entirely accurate with first and last names being interchanged.  I also like sorting my books into genres or themes.  It may be there, I confess I have just added a few books and have to play with this app some more. 

The developers have really done a great job and it will become one of my favorite apps for reading.  I would love to hear what others have to say.  Marvin has no ratings yet in the App Store. 

I don't have any Dropbox files and haven't needed it yet, but I imagine that it won't be long before I start to use it.  Marvin sure is a great little app well worth having on the iPad.  I wish it was available for my iPod too as I read a lot of books on the iPod.