if I don't mess with the JTAG fuses, are there any other pins that could be used for analog IN?
I believe you can use the PORTF4..7 for analog input regardless of the JTAG fuses. You only have to turn off JTAG if you want to use them for digital IO.
I should probably put some names on those pins for analog use, the digital IO names, JTAGPINn, won't work for analogRead, and as long as ADC0..3 are named, ADC4..7 probably ought to be as well.
are there problems using the joystick as input pins? I remember seeing somewhere something about this.
You can use the joystick pins for general IO, as long as you keep in mind that if you use the joystick you'll short to ground whatever you have attached to the pin.