A## pins support analogRead() (pinMode() not required).
D## pins support digitalRead() and digitalWrite() (along with our own digitalToggle() if you just want to switch the output value) if you set the pin function with pinMode().
TX0/RX0 are available using Serial0.
TX2/RX2 are available using Serial2.
I use those extensively with an FTDI USB-Serial board for debugging.
For SPI, if you want to use Serial2 also, you can select ALT SPI in the Arduino IDE Tools menu, and then R13 and R14 are used instead of L06 and L08. Any D## pin can be used as chip select for SPI.
Any of the WU## pins can be used for deep sleep wakeup if configured as inputs and specified as wake up pins.
Any D## pin can be used with attachInterrupt to wake from normal (not deep) sleep.
L14 is a true analog output when used with analogWrite. All other pins marked with a P support analogWrite using PWM output.