No ugly fonts.

In my /etc/make./conf I have truetype and gtk2 for my USE variable. Fonts should generally look good with this. The gentoo website warns that gtk2 in /etc/make.conf might be dangerous, but I have not had any huge problems. If available, I would recommend gtk2 apps over their gtk1 counterparts especially if anti-aliased fonts are important.
USE="X gtk gnome gtk2 truetype"
 a snippet from /etc/make.conf
Microsoft truetype fonts
I can not remember if I installed additional Microsoft fonts or if they came with some package I installed. Nevertheless, take a look at http://corefonts.sourceforge.net/ if you would like to use Microsoft's truetype fonts in linux. Additionally, you may also copy your fonts from your existing windows installation. ttmkfdir, a utility for generating fonts.scale , is useful for installing these fonts. After the fonts are in the proper location (/usr/X11R6/lib/X11/fonts for me), you need to add the directory where your new fonts reside into your XF86Config file.
Section "Files
FontPath "/usr/X11R6/lib/X11/fonts/microsoft/"
  Add your truetype fonts directory to XF86Config file (/etc/X11/XF86Config)
Gnome
What were those miscreant gnome people thinking? Default fonts in gnome don't look so hot.
$ gnome-control-center &
Select "Font"
Type Font Size
Application font Tahoma 12
Desktop Font Tahoma 12
Terminal Font Andale Mono 12
Here are my choices for fonts

A screenshot of my gnome panel after tweaking.

Sawfish
Change the font in sawfish interactively with sawfish-ui (sawfish configurator) or edit ~/.sawfish/custom. Take a look at the sawfish widgets and fonts near the top in a screenshot of my terminal. The sawfish theme is cryoGUI.
(quote default-font) (quote "-microsoft-tahoma-medium-r-normal-*-*-120-*-*-p-*-koi8-ru")
 Edit ~/.sawfish/custom and add the above line
Mozilla
Edit -> Preferences -> Appearance -> Fonts
Proportional Sans Serif 16
Sans-Serif Arial
Monospaced Andale Mono 12
My mozilla fonts

I also changed the "Minimum font size" to something larger. Here are before and after screenshots of mozilla after font configuration. The banner ad is blocked by privoxy, which I will get to in a bit.

Terminal
I use aterm, but you can use the -fn flag for xterm too. While this is the same picture as the sawfish screenshot, pay attention to the monospaced font.
$ aterm -fn "-monotype-andale mono-medium-r-normal--12-120-75-75-m-80-koi8-ru"
 This is part of the command I run for aterm
OpenOffice
It was not necessary for me to put in additional effort to get OpenOffice fonts looking good, but here are some links I found about fixing font problems in OpenOffice.
http://forums.gentoo.org/viewtopic.php?t=27260&sid=1ac3f3241f36a932c82e9c28e3f188a7
http://www.openoffice.org/FAQs/fontguide.html

I believe the only tip I needed to follow from the openoffice troubleshooting guide was the bit about changing the user interface fonts. Several months ago while executing the tip from the first link (export LD_PRELOAD="/usr/lib/libfreetype.so"), my fonts in openoffice indeed did look better. However, the same thing recently did not alter anything. Openoffice with my defaults already looks nice. By the way, I use the openoffice precompiled binary provided by the ebuild app-office/openoffice-bin-1.0.2.