If you open the reference design in Eagle you can File->Export... Partlist to get a text file like this:
Partlist
Exported from Arduino_MEGA2560_ref.brd at 6/27/12 21:18
EAGLE Version 6.1.0 Copyright (c) 1988-2012 CadSoft
Assembly variant:
Part Value Package Library Position (mil) Orientation
ADCH 1X08 pinhead (3250 100) R0
ADCL 1X08 pinhead (2350 100) R0
C1 22p C0603-ROUND SmartPrj (1100 525) R180
C2 100n C0603-ROUND SmartPrj (600 700) R0
C3 100n C0603-ROUND SmartPrj (1100 1750) R0
C4 100n C0603-ROUND SmartPrj (1520 280) R0
C5 100n C0603-ROUND SmartPrj (2320 1550) R0
C6 100n C0603-ROUND SmartPrj (1576.5748 1197.59843) R180
C7 100n C0603-ROUND SmartPrj (1100 700) R0
C8 100n C0603 rcl (600 1000) R0
C9 100n C0603-ROUND SmartPrj (850 1325) R0
C10 1u C0603-ROUND SmartPrj (475 1725) R180
C11 100n C0603 rcl (850 1000) R0
C12 100n C0603-ROUND SmartPrj (850 700) R180
C13 100n C0603-ROUND SmartPrj (1100 850) R0
C14 22p C0603-ROUND SmartPrj (1575 450) R90
C15 22p C0603-ROUND SmartPrj (1575 700) R270
C16 22p C0603-ROUND SmartPrj (600 1075) R180
C17 22p C0603-ROUND SmartPrj (850 1075) R0
COMMUNICATION 1X08 pinhead (3050 2000) R180
D1 M7 SMB diode (725 475) R180
F1 500mA L1812 rcl (175 1000) R180
GROUND SJ jumper (425 1300) MR180
IC1 MC33269ST-5.0T3 SOT223 linear (340 700) R90
IC2 MC33269D-5.0 DPACK linear (275 700) R90
IC3 ATMEGA2560-16AU TQFP100 atmel-2005 (2000 1116) R0
IC4 ATMEGA8U2-MU QFN32 atmel (720 1500) R90
IC5 LM358D SO08 linear (720 850) R270
IC6 LP2985-33DBVR SOT23-DBV texas (1100 991) R180
ICSP ICSP 2X03 pinhead (2555 1100) R270
ICSP1 ICSP 2X03 pinhead (720 1820) R180
JP1 1X01 pinhead (3700 2000) R0
JP2 1X01 pinhead (3800 2000) R0
JP3 1X01 pinhead (3700 300) R0
JP4 1X01 pinhead (3800 300) R0
L YELLOW CHIP-LED0805 led (1100 1650) R90
L1 BLM21 0805 wuerth-elektronik (325 1780) R180
ON GREEN CHIP-LED0805 led (3000 1450) R90
PC1 47u PANASONIC_D rcl (800 225) R90
PC2 47u PANASONIC_D rcl (1100 225) R90
POWER 1X06 pinhead (1550 100) R0
PWMH 1X08 pinhead (1290 2000) R180
PWML 1X08 pinhead (2150 2000) R180
Q1 16MHz QS special (720 1200) R180
Q2 16MHz QS special (1450 575) R270
R1 1M R0603-ROUND SmartPrj (1575 575) R90
R2 1M R0603-ROUND SmartPrj (725 1075) R0
R3 27R R0603-ROUND SmartPrj (1650 575) R270
R4 27R R0603-ROUND SmartPrj (600 1325) R180
RESET TS42 TS42 st-mod v1.4 (2920 1100) R90
RESET-EN SJ jumper (1100 600) R0
RN1 10K CAT16 resistor-dil (3175 1450) R270
RN2 22R CAY16 resistor-dil (475 1500) R90
RN3 1k CAY16 resistor-dil (1100 1550) R270
RN4 1k CAY16 resistor-dil (1100 1225) R90
RN5 10K CAT16 resistor-dil (725 650) R90
RX YELLOW CHIP-LED0805 led (1100 1350) R90
T2 FDN340P SOT-23 zetex (375 1000) R270
TX YELLOW CHIP-LED0805 led (1100 1450) R90
U$2 FIDUCIALMOUNT FIDUCIA-MOUNT SmartPrj (2789 1503.62992) R0
U$3 FIDUCIALMOUNT FIDUCIA-MOUNT SmartPrj (105 95) R0
U$4 FIDUCIALMOUNT FIDUCIA-MOUNT SmartPrj (780 2000) R0
U$5 FIDUCIALMOUNT FIDUCIA-MOUNT SmartPrj (2000 1116) R0
UBOOT SJ jumper (830 1610) MR90
X1 DC21MMX DC-21MM powersupply (210 330) R90
X2 PN61729 SmartPrj (150 1500) R270
XIOH 2X08 pinhead (3750 1550) R90
XIOL 2X08 pinhead (3750 750) R90
Y1 16MHz RESONATOR SmartPrj (1450 575) R270
Y2 16MHz RESONATOR SmartPrj (720 1200) R180
Z1 PGB1010604 CT/CN0603 varistor (475 1400) R0
Z2 PGB1010604 CT/CN0603 varistor (475 1600) R0