Hey Guy,
We use Skype as part of our corporate enviroment. To answer your questions:
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1) Should the IT Department create these accounts or leave it to the individual user?
If you want uniformity that allows individuals in your company to find others (see below answer), I would have one individual create them, regardless of whether they're in the IT department or not.
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2) What naming conventions work best for finding co-workers? For example CompanyX:john.doe
We use our company name first, as you use in your example, and find it works well. Our code is onstate.flastname.
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3) What other policies / guidelines has your company put in place for skype use?
We're pretty open with our policies. Others on here might be able to lend some help in terms of large enterprises that use it.
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4) Any other advice...;-)
Make sure you read the recent questions and concerns of other business users on this board and do your best to avoid them. And if you want to extend your Skype presence to your customers so that they can find employees in your company using any device from any location, check out OnState's
Skype Solutions.
And good luck!