Hi, I just got my Duemilanove shipped (^^), and I played with it - first thing i had idea of was "blink a LED with delay given by computer": So I found this: http://arduino.cc/en/Tutoria/PhysicalPixel and edited it so it blinks the led, with "delay(incomingByte)" - it had weird delays, so I included a function to print the variable, and I figured out that it takes the ASCII values, even if I supply numbers 
:everything was happy, till i wanted to upload another program.
Binary sketch size: 472 bytes (of a 14336 byte maximum)
avrdude: stk500_getsync(): not in sync: resp=0x87
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x06
On IRC, i was given the advice to burn the bootloader:
avrdude: stk500_getsync(): not in sync: resp=0x00
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x00
I am not sure if I caused it by the code that "blocks" serial input, since the autoreset feature.
Any ideas?
EDIT: Wow, fixed by itself... :o I did a pack of things, like unplgging the board for a few minutes, reinstallation of IDE... not sure which helped, but it works now