Or, if possible, use formatting to differentiate (like this :-) )

I disapprove of emoticons

Hm... just one example from http://www.apa.org/monitor/feb06/egos.aspx

... Kruger and his colleague Nicholas Epley, PhD, of the University of Chicago, have published research that helps explain why these electronic misunderstandings occur so frequently. In a study in the December Journal of Personality and Social Psychology (Vol. 89, No. 5, pages 925-936), they find that people overestimate both their ability to convey their intended tone-be it sarcastic, serious or funny-when they send an e-mail, as well as their ability to correctly interpret the tone of messages others send to them.

I think a smiley is easiest to type to say, "Hey, I'm just kidding" ;-)