Just to mention, I ran those commands on Debian 6.0.1 Squeeze with no xorg.conf
So, first I ran
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cvt 1280 1024
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$ cvt 1280 1024
# 1280x1024 59.89 Hz (CVT 1.31M4) hsync: 63.67 kHz; pclk: 109.00 MHz
Modeline "1280x1024_60.00" 109.00 1280 1368 1496 1712 1024 1027 1034 1063 -hsync +vsync
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xrandr --newmode "1280x1024_60.00" 109.00 1280 1368 1496 1712 1024 1027 1034 1063 -hsync +vsync
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$ xrandr
Screen 0: minimum 320 x 200, current 1024 x 768, maximum 2048 x 2048
VGA1 connected 1024x768+0+0 (normal left inverted right x axis y axis) 0mm x 0mm
1360x768 59.8
1024x768 60.0*
800x600 60.3 56.2
848x480 60.0
640x480 59.9 59.9
1280x1024_60.00 59.9
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xrandr --addmode VGA1 1280x1024_60.00
Anyways, It was good until it lasted. After reboot I lost that mode and I had again to type last two commands.
But, as sugested by someone, since I am using gnome, I edited /etc/gdm3/Init/Default file, and added
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xrandr --newmode "1280x1024_60.00" 109.00 1280 1368 1496 1712 1024 1027 1034 1063 -hsync +vsync
xrandr --addmode VGA1 1280x1024_60.00
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exit 0