I recently read this statement in one of the posts.
Timer0 is used for the millis timer and the delay function. These are fundamental functions in the arduino environment and breaking these by modifying timer0 would make your code arduino unfriendly.
Is there any documentation on ALL of the resources that the standard Arduino core software uses so that I know what remains for use in my sketches?
Timer0 and the associated interrupt are about it for really core functionality.
PWM outputs use TIMER1 and TIMER2 as well, but you can easily override those if you don't use PWM.
The UART and associated interrupts are used by the Serial.xxx functions, and it's possible for the USB chip (also connected to the Serial RxD/TxD pins to interfere with use of digital 0/1 for some applications.)
Digital13 has the LED, which can also interfere with some uses.
2k of flash is occupied by the standard bootloader.
Don't forget that your distribution of the Arduino environment includes ALL of the source code for the AVR, so if you're really worried, you can read the source...
I should also say that the Arduino core includes handlers for Int0 and Int1. These are just shells designed to chain to user-provided functions, but it might make it difficult to include highly-tuned assembler implementations of INT0 and INT1 ISRs...