When I use those applications I usually just send links to webpages I have saved in My Favorites. Quite a few times I've even sent my roommate pictures and website links, even though we're an arm's length away from each other. Sometimes clicking is easier than reading the url out.
I can see them using a chat program during work or when they need to send a link to each other quickly. And, like you said, they're probably both fast typists.
A work environment would be especially interesting. Can't you just see them researching together? However, it makes Clark less likely to hover around Lois's desk. *Thinks* You know, it would be interesting to see her typing to a friend, and when Clark sees the message he gets jealous. *Evil grin*
On the same topic, can you see Clark and his parents talking via the Internet? That would make an amusing little vignette, I would think . . . Definitely cut down on phone bills.
