Before I compare the current devices, some background. I've been reading e-books on handheld devices since 1995 and I've owned (or own) all of the following: various cell phones; Apple Newton; Handspring Visor; Palm Pilot 1000, M125, T2, TX, and Zire 72; Nook (e-ink); iPhone; and iPad. Out of all of them my preference would be (in order): iPad, iPhone, Palm TX, and Nook.
I prefer the color screen devices since I'm seldom reading them in direct sunlight and can adjust the backlighting, screen color, and text color to get a comfortable reading setting. I don't find the LCD screen to be a problem once I get my settings correct so I don't have the headache problem many people complain about. The iPad is my choice for anything with detailed graphics due to the larger screen. My iPhone has a lot loaded in it and I can always find something to read and both work with Kindle and Nook books. Both also allow me to do MUCH more than just read. The TX is my fallback as it has a decent color screen, I can convert most non-DRM books to work with it, and it is not much larger than the iPhone. My Nook is my device of last resort. It doesn't handle graphics well, is only so-so with PDFs (even all text ones), the contrast is low, and I have to carry an additional light if the place I'm reading has less than ideal light. I've also found that using the external light always seem to cause either a reflection, glare or hotspot somewhere on the screen. I also think the Nook has a slow to use and fairly poor user interface when compared to my other devices. I have never used a Kindle but I know people that have them and they have UI complaints also.
Stanza is my preferred reader on the iPhone and I'm going back and forth between Stanza and iBooks on the iPad. The Nook is stuck with whatever B&N puts out and the limits of the device. The Palm TX suffers from the fact that development is dead but I have 4 different readers there so I'm covered until it finally dies.