Everything I'm involved with uses email through a ticket system (or god forbid the telephone! ) as the main point of contact. In each case though, we've got our IM's (Google Talk, AIM, Yahoo, ICQ and MSN... I think Skype is the only one I don't have) and some customers do use them every now and then for quick things - for some things, they are GREAT to use as it avoids the 'back and forth' with emails required to get things sorted and works out much quicker and so better for everyone. Other things they aren't so good for, and so that’s when I nudge them towards email and the ticket system.

Having lots of different contact points is a good thing I think. How you use them is the important bit - ensure you know what each is good for, and don't hesitate to politely ask customers to drop in a ticket (or conversely, open an IM with you) so that you can deal with their issue(s) as efficiently as possible.