Sounds like a fuel/air mixture issue. Backfire through your intake/TB can be caused by a few things. Lets start with free stuff, and work towards more in-depth/expensive.
1- Double check your firing order on your plug wires. Very common after a tune up to get a couple crossed, and have it spark on a cylinder that isn't sealed, thus sending fire through the throttle body.
2- Check your timing. Advanced or retarded timing will cause spark at the incorrect time, thus failing to ignite the fuel appropriately.
3- Check your fuel pressure. A rich system can cause backfire through the TB, whereas lean can cause backfire at the tailpipe. Check these:
A- Fuel filter
3- A faulty/misreading O2 sensor can cause a lean/rich run cycle.
4- An intake valve stuck open can cause backfire through the TB. Fuel and air does not get properly sealed into cylinder during ignition, causing combustion in the intake.
Hope this is helpful, and I didn't go too in-depth. Good luck.