tl;dr: Succesfully troubleshooted sketch upload to an Arduino Ethernet, but why did I have to change in boards.txt ethernet.upload.protocol=stk500 to arduino?
(This is verbose in the hopes of providing hints for other people having problems)
I got a new Arduino Ethernet this week. I already have a FTDI-USB cable from Adafruit, as well as their USBTinyISP programmer. That Ard'Ethernet page is pretty lacking in instructions on how to program it 
I'm on Ubuntu Linux, after the usual driver trouble (remember to modprobe ftdi_sio for the cable if it's not loaded automatically, remember to add the udev rules for usbtinyisp so that you don't need to be root to run avrdude), I can read from the arduino [1]. The output is at the end of this post.
I got the new boards.txt file from the bottom of the Arduino Ethernet page, I assumed the new version it provided for 1.0Beta also applied to 1.0 full. Was I wrong? Anyhow, I noticed that it changed the ethernet.upload.protocol between "arduino" and "stk500" for a number of boards (sometimes setting it to stk500, sometimes arduino).
Though I had selected "Arduino Ethernet (with USB2Serial module)" and the right serial port (/dev/ttyUSB0), I couldn't upload to the arduino as I was getting this error:
Binary sketch size: 14246 bytes (of a 32256 byte maximum)
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.
Eventually I thought of replacing the ethernet.upload.protocol setting in boards.txt from "stk500" to "arduino", and it finally worked. But why did I have to do that? Why is the setting in the website-supplied file wrong? What is the advantage of the stk500 uploader?
Extra info:
This is the output of checking the Arduino through the USB-FTDI cable (yay bootloader!):
avrdude -c arduino -p m328p -P /dev/ttyUSB0 -v
avrdude: Version 5.10, compiled on Mar 23 2010 at 15:05:31
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "/etc/avrdude.conf"
User configuration file is "/home/jlargentaye/.avrduderc"
User configuration file does not exist or is not a regular file, skipping
Using Port : /dev/ttyUSB0
Using Programmer : arduino
AVR Part : ATMEGA328P
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
eeprom 65 5 4 0 no 1024 4 0 3600 3600 0xff 0xff
flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
lock 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
Programmer Type : Arduino
Description : Arduino
Hardware Version: 3
Firmware Version: 4.4
Vtarget : 0.3 V
Varef : 0.3 V
Oscillator : 28.800 kHz
SCK period : 3.3 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0x1e950f
avrdude: safemode: lfuse reads as 0
avrdude: safemode: hfuse reads as 0
avrdude: safemode: efuse reads as 0
avrdude: safemode: lfuse reads as 0
avrdude: safemode: hfuse reads as 0
avrdude: safemode: efuse reads as 0
avrdude: safemode: Fuses OK
avrdude done. Thank you.
And this is the output through USBtinyISP:
avrdude -c usbtiny -p m328p -v
avrdude: Version 5.10, compiled on Mar 23 2010 at 15:05:31
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "/etc/avrdude.conf"
User configuration file is "/home/jlargentaye/.avrduderc"
User configuration file does not exist or is not a regular file, skipping
Using Port : /dev/parport0
Using Programmer : usbtiny
AVR Part : ATMEGA328P
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
eeprom 65 5 4 0 no 1024 4 0 3600 3600 0xff 0xff
flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
lock 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
Programmer Type : USBtiny
Description : USBtiny simple USB programmer, http://www.ladyada.net/make/usbtinyisp/
avrdude: programmer operation not supported
avrdude: Using SCK period of 10 usec
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.01s
avrdude: Device signature = 0x1e950f
avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as DE
avrdude: safemode: efuse reads as 5
avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as DE
avrdude: safemode: efuse reads as 5
avrdude: safemode: Fuses OK
avrdude done. Thank you.
[1] I was afraid I damaged the board by misplugging the ISP connector: the red line must be oppposite to the SDCard connector. I had missed the teensy dot on the board. I was also very confused for a while how to connect the FTDI cable, and resorted to checking the board to identify which pin went to the ground plane, I had missed the tiny "blk" writing. The silkscreening could afford to be more obvious, as I've had similar issues with other boards such as the power connector for ArduinoBT.