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xdpyinfo | grep -B2 resolution
screen #0:
dimensions: 1920x1080 pixels (597x336 millimeters)
resolution: 82x82 dots per inch

Section "Monitor"
Identifier "Monitor0"
DisplaySize 346 195 # In millimeters
EndSection

Section "Screen"
Identifier "Screen0"
Monitor "Monitor0"
EndSection

В строке DisplaySize нужно указать размеры своего дисплея в миллиметрах рассчитанные в DPI калькуляторе. После перезагрузки проверяем вывод xdpyinfo значение resolution должно быть максимально близким к рассчитанным.

$ cat /etc/X11/xorg.conf.d/90-monitor.conf
Section "Monitor"
Option "UseEdidDpi" "false"
Identifier "Monitor0"
DisplaySize *** ***
EndSection

Section "Screen"
Identifier "Screen0"
Monitor "Monitor0"
EndSection

Actually you should do 2 things to set your DPI correctly.

I'll explain on example. I'm using Ubuntu LTS 12.04 with Gnome Classic and I've got a monitor with resolution 1680x1050. Let's check my starting settings: xdpyinfo | grep dots reports 96x96 dots , xrdb -query | grep dpi reports Xft.dpi: 96 , cat /var/log/Xorg.0.log | grep DPI reports some weird settings NOUVEAU(0): DPI set to (90, 88).

Let's calculate optimal DPI for my monitor. Actual size of the screen in centimetres can be found with xrandr | grep -w connected or with the long ruler by hand. In my case: X = 47.4cm ; Y = 29.6cm. Divide them by 2.54 to get the size in inches: X ~ 18.66in ; Y ~ 11.65in. Now divide actual dots amount (based on your resolution) by the size in inches: X = 1680/18.66 ~ 90dpi ; Y = 1050/11.65 ~ 90dpi. So my real dpi is 90. Let's start fixing it:

1) Run gksudo gedit, open /etc/lightdm/lightdm.conf and add a parameter under [SeatDefaults] section:

xserver-command=X -dpi 90

Restart your computer or restart X. Now xdpyinfo | grep dots will report 90x90 dots and cat /var/log/Xorg.0.log | grep DPI will also show the desired setting.

Alternative variant, which doesn't depend on lightdm: create a file 77set_dpi somewhere (in home folder for example) and put the line in it:

xrandr --dpi 90x90

Then run sudo mv ~/77set_dpi /etc/X11/Xsession.d/ and restart. The result should be the same (though in my case it won't fix the setting shown in Xorg log).

2) In GNOME3 DPI setting is hardcoded to 96 and cannot be changed directly, but the text can be scaled instead. Calculate the desired multiplier: desired_DPI / 96 (in my case 90/96 = 0.9375). Now run the command (or use dconf if you prefer):

gsettings set org.gnome.desktop.interface text-scaling-factor 0.9375

Changes will be applied immediately and xrdb will also be updated on the fly. xrdb -query | grep dpi will report the desired Xft.dpi: 90.

Now DPI is correctly set for the monitor.

P.S. There is another method to fix DPI setting much more difficult than double-step method mentioned above: download the sources of 'gnome-settings-daemon', fix the hardcoded setting in it and recompile them as mentioned in the guide http://blog.drtebi.com/2012/12/changing-dpi-setting-on-gnome-34.html. I tried it also, but the result is absolutely the same.

The DPI of the X server is determined in the following manner:

The -dpi command line option has highest priority.
If this is not used, the DisplaySize setting in the X config file is used to derive the DPI, given the screen resolution.
If no DisplaySize is given, the monitor size values from DDC are used to derive the DPI, given the screen resolution.
If DDC does not specify a size, 75 DPI is used by default.

In order to get correct dots per inch (DPI) set, the display size must be recognized or set. Having the correct DPI is especially necessary where fine detail is required (like font rendering). Previously, manufacturers tried to create a standard for 96 DPI (a 10.3" diagonal monitor would be 800x600, a 13.2" monitor 1024x768). These days, screen DPIs vary and may not be equal horizontally and vertically. For example, a 19" widescreen LCD at 1440x900 may have a DPI of 89x87. To be able to set the DPI, the Xorg server attempts to auto-detect your monitor's physical screen size through the graphic card with DDC. When the Xorg server knows the physical screen size, it will be able to set the correct DPI depending on resolution size.

To see if your display size and DPI are detected/calculated correctly:

$ xdpyinfo | grep -B2 resolution

Check that the dimensions match your display size. If the Xorg server is not able to correctly calculate the screen size, it will default to 75x75 DPI and you will have to calculate it yourself.

If you have specifications on the physical size of the screen, they can be entered in the Xorg configuration file so that the proper DPI is calculated:

Section "Monitor"
Identifier "Monitor0"
DisplaySize 286 179 # In millimeters
EndSection

If you only want to enter the specification of your monitor without creating a full xorg.conf create a new config file. For example (/etc/X11/xorg.conf.d/90-monitor.conf):

Section "Monitor"
Identifier "<default monitor>"
DisplaySize 286 179 # In millimeters
EndSection

If you do not have specifications for physical screen width and height (most specifications these days only list by diagonal size), you can use the monitor's native resolution (or aspect ratio) and diagonal length to calculate the horizontal and vertical physical dimensions. Using the Pythagorean theorem on a 13.3" diagonal length screen with a 1280x800 native resolution (or 16:10 aspect ratio):

echo 'scale=5;sqrt(1280^2+800^2)' | bc # 1509.43698

This will give the pixel diagonal length and with this value you can discover the physical horizontal and vertical lengths (and convert them to millimeters):

echo 'scale=5;(13.3/1509)*1280*25.4' | bc # 286.43072
echo 'scale=5;(13.3/1509)*800*25.4' | bc # 179.01920

Note: This calculation works for monitors with square pixels; however, there is the seldom monitor that may compress aspect ratio (e.g 16:10 aspect resolution to a 16:9 monitor). If this is the case, you should measure your screen size manually.
Setting DPI manually

DPI can be set manually if you only plan to use one resolution (DPI calculator):

Section "Monitor"
Identifier "Monitor0"
Option "DPI" "96 x 96"
EndSection

If you use an NVIDIA card, you can manually set the DPI adding the options bellow on /etc/X11/xorg.conf.d/20-nvidia.conf (inside Device section):

Option "UseEdidDpi" "False"
Option "DPI" "96 x 96"

For RandR compliant drivers, you can set it by:

xrandr --dpi 96

See Execute commands after X start to make it permanent.

Note: while you can set any dpi you like and applications using Qt and GTK will scale accordingly, it's recommended to set it to 96, 120 (25% higher), 144 (50% higher), 168 (75% higher), 192 (100% higher) etc., to reduce scaling artifacts to GUI that use bitmaps. Reducing it below 96 dpi may not reduce size of graphical elements of GUI as typically the lowest dpi the icons are made for is 96.