Dr. Taylor at Poliblog has defended the use of emoticons because they better enable to e-mail to express tone. I've given a lot of thought to that issue in the past, and I'm a bit ambivalent about that argument.
The English professor in me wants to point out pre-print writing conveyed tone for millennia without the use of emoticons, and print culture managed to do it for half a millennium. With that in mind, emoticons seem to be taking the place of older, subtler methods of conveying tone.
That being said, punctuation is itself a guide toward expressing tone in the text, through something so subtle as comma placement or so unsubtle as an exclamation mark. Once we entered print culture, people began to mix font types in an effort to express tone, such as bolding or italics. I often find the inability to underline in Blogger (without also hyperlinking) awkward, and end of giving italics double duty.
As I mentioned in the original post, the oral and the written seem to be re-converging, and I think emoticons are an effort to make this tone feel more oral. It is certainly true that people read tone in e-mails differently than they do in other texts. So, an anecdote ...
When I was a graduate student, my advisor suggested that I ask someone to be on my dissertation committee because of her area of expertise, even though I didn't know that professor very well (I'll call her Dr. X here). I agreed that it was a good idea, and sent an e-mail to set up an appointment. The e-mail was short and business-like, just a couple of lines, something like:
Dear Dr. X,
I am putting together my dissertation committee, and would like to have you on it, if possible. Would it be possible for me to make an appointment to discuss it with you?
The above is from memory, but it's pretty close. Dr. X was infuriated by the e-mail and went to my advisor with it. She said that the e-mail had a "hostile" tone, and that she could never work with someone as offensive as me. My advisor tried to smooth the ruffled feathers. I was bewildered, and re-read the e-mail over and over to try to find the hostile tone. My advisor couldn't figure it out either. I have often wondered if the medium of e-mail was partly to blame for the misunderstanding.
In way of epilogue, Dr. X apparently forgot all about the incident, and a couple of years later asked my why I never asked her to be on my committee. I didn't remind her, and instead stammered some lame excuse.