default font size is normally determined by how X is launched.
$ ps fuwax
For me I get:
/usr/bin/startx -- -dpi 100
Because that's how I start X. If you're running a display manager, you probably need to modify it's configuration file (/etc/kde3/kdm/kdmrc, yada yada yada). It's probably already using -tcp nolisten as an X parameter. I think 75 dpi is the default, which renders small. There used to be a condition where you had to specify 96 dpi or 100 dpi at the browser level to have font sizes more closely match those of IE in windows. For all intents and purposes, the higher the DPI (dots per inch) you specify the larger the default font(s). Normally 100 is good enough and expected by most applications.
$ egrep -r -i "-tcp nolisten" /etc/*
Also, you can specify some of that at the application level. Like for mplayer you can give it a default font and font-size. In firefox or mozilla you can go to about:config and change a parameter there. I think it's also in Edit -> Preferences. i.e. More than one way to skin a cat. I tend to override the default myself because my mom is old and windows makes here angry / moody.
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