To summarize (just trying to help others reading this thread): AT90USB162 has
- a native full-speed (12 MBit/2) USB interface, with 176 bytes USB DPRAM for four programmable endpoints and one (endpoint 0) for control transfers, and supports USB packets up to 64 bytes
- by default (from factory), Atmel's USB DFU bootloader installed
- a calibrated internal oscillator, 8 MHz ± 1% at 3.3V VCC at 25°C/77°F; but not precise enough to allow the USB to work
If you intend to use the USB bus, you need a 8 MHz or 16 MHz crystal, better than ±0.25%. The microcontroller is usable without a crystal or resonator, as it has a built-in 8 MHz oscillator it uses when booting, but it is not precise enough for the USB bus to work.
You can use the USB +5V (VBUS, UVCC on the microcontroller) directly, as the maximum VCC is 5.5V (which is outside valid USB VBUS range).
If you want to run at 3.3V, you need a voltage regulator, that regulates the USB bus voltage down to 3.3V (connected to VCC on the microcontroller).
If you want to run from external 3.4V - 5V power, disconnect USB VBUS completely, and connect UVCC and VCC on the microcontroller to your external power supply.
If you want the microcontroller to be able to run from either external 5V power when not connected to USB, or from USB 5V when connected, use a pair of low-drop Schottky diodes (500mA) with the cathodes connected to microcontroller VCC, one anode to external 5V supply, and the other anode to USB VBUS, with USB VBUS also connected to UVCC. (Internally, UVCC is connected to a 3.3V regulator, that is used to supply the 3.3V level USB signals.)
If you want to run at 5V, you'll need a crystal or resonator (typically 8 MHz or 16 MHz), as the internal oscillator is not calibrated for 5 V. You do not need a voltage regulator, as you use the 5V USB VBUS or UVCC directly.
The minimum circuit for 5V/16MHz operation needs a 16 MHz crystal and its two caps (10 pF, I believe), one 1µF cap from UCAP to ground, 0.1µF and 1µF bypass capacitors (from VBUS, UVCC, AVCC, VCC, all connected together, to ground), and two 22Ω resistors (one between USB D+ and microcontroller D+, and the other between USB D- and microcontroller D-).