Perhaps the most notorious application as far as fonts are concerned is the dreaded Netscape. However, there is a fairly simple procedure to attack Netscape font ugliness. The main problem is that Netscape wants to use 75dpi fonts which is typically too small. You can fix this by specifying the appropriate X resources in your .Xdefaults file:
Netscape*documentFonts.sizeIncrement: 20
Netscape*documentFonts.xResolution*iso-8859-1: 100
Netscape*documentFonts.yResolution*iso-8859-1: 100
The number 100 can be chosen arbitrarily. For example, if you like your fonts really large, like I do, then you may want to use 150 instead.
The other essential tip with regard to addressing Netscape font ugliness is this -- get the Microsoft font pack. These fonts are widely used and it makes an enormous difference if you have ( or don't have ) those fonts.