Tinkertool took care of most of the too-small fonts (are any Apple designers over 40?), but the white text on my preferred light desktop is bad. Linux GTX has a rather tricky file to hand-edit to fix a similar bad default. Does Yosemite have any well-hidden way of changing the desktop icon font color?
As far as I know, it is not possible to change the color of the system font. The system graphic interface files are under the license protection of Apple's user agreement and they are well guarded with encryptions. This also results in the lack of capacity of turning off full screen animation, and other unfortunate unique OSX graphic interface design features and behaviors.
This doesn't do exactly what you want, but it might make the colors more bearable.
System Preferences > Accessibility > Display and play around with
Invert Colors and
Enhance Contrast options.
If you want to achieve the effect of making your desktop font black, you can try turning on the Invert Colors and Use Gray Scale options.
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I would recommend a better workaround, however. I believe the reason your white font looks bad is because you have your background set to something light. I had a similar issue too until I set my background to something more neutral. Try setting it to a solid color like a shade of brown, or a dull medium blue. Of course, dark grey or black would also work, but I personally don't like the colorless, depressing look of a plain black or grey background.
I've run into that too and ended up using an app called NerdTool to create semi-permanent bars behind my logos (also helped with the icons that I had changed that were partially transparent and completely disappeared against dark backgrounds.
In this case, I took a frame (ie I googled 3D frame and downloaded an image that looked like it might look ok). I used NerdTool to put the image on the wallpaper and set the size to what I wanted (took some finagling). That's how I got the white bar on top. Then I took a screen shot of a part of my screen that was black, imported that into NerdTool, and stretched and positioned it to be under the letters to make those pop out.
NerdTool can be a little daunting if you don't know the command line, but for this circumstance you don't actually touch terminal.
Of course this will only work for files that you plan on keeping put on your desktop and isn't a great solution if your shuffling stuff around a lot, but for me, the files in the screen shot I included are ones that I use frequently and are going to stay there.
I know this isn't a fix all, but it's something. Hope this helps someone.
You can create your own user .css file to modify the default fonts when using Safari on Yosemite