Before I start typing: Disclaimer applies. I'm not a tax professional, this is just the way I understand things.
Your stipend and money paid on your behalf for health insurance is federally taxable, but not subject to self-employment tax--which is what normally includes FICA, social security, etc etc etc etc that shows up on a normal paycheck. That means you pay income tax, usually about 10% of your income quarterly. Whether is subject to local or state income tax depends on your jurisdiction. At UPenn, our stipends are not subject to state or Philadelphia tax.
You can deduct under the lifelong learning credit all "mandatory" educational expenses--fees, books, equipment, etc... Under that credit, up to 20% of a maximum of $2,000 can be deducted from your tax owed.