One format that isn't good for ebook readers is pdf. I have a lot of electronic roleplaying products in pdf format. Most of these have double columns.
Now, the text actually does reflow so I'm reading one column at a time, but there can be some very odd results.
Chaosium's monographs are mostly readable on the Sony. Maps and character sheets don't always come out readably, and sometimes not at all, but the text is pretty clean. The places I found missing text are the places where text is just plain missing in the original file.
Delta Green: Targets of Opportunity is a bit of a problem. Oh, on my laptop, it reads just fine. On the Sony, text will be out of order, bits from one column getting mixed in with another, so each page is like a jigsaw puzzle. This is not good.
And forget the Dresden Files books on the Sony! Again, my laptop handles them fine, but here? So, the conceit is that the game was written by characters in the book, and they're all commenting in post-it notes on the manuscript. This makes for a very confused Sony, with the material out of order. But, what about the regular text?
Well, I'm not sure. I suspect it's like the Delta Green book, but 400+ page full color pdf files are slooow on the Sony. I hit the button to turn the page, read the page I'm on, and still have to wait a while before the next 5 inches of text appear.
None of this, you understand, is anything Sony's doing wrong. The pocket reader was not designed with files like this in mind. Unfortunately, attempts to use calibre to tweak the files resulted in material significantly less readable than the original.
It might be worth dropping ArcDream and EvilHat a line to see if there is a text only version available. I tend to doubt it, and in both cases, I have the hard copy pre-ordered. It'd jut be really neat to be able to read them on the pocket reader. But, so it goes. I've still got several monographs to read.