I am preparing payroll for a small non-profit. Two of their employees also received stipends during the year, but not while employed. Do I include the stipend amount on the W-2? Or would they go on a 1099-Misc?

Here are the details:

Employee 1: Employee wages = $2831 + $300 Stipend
Employee 2: Employee wages = $2921 = $475 Stipend

Unless the stipend has a specific purpose, it is taxable income.