You can specify fonts by using a custom config file for FCKeditor, you can see from this setting in Web.config that it uses /ClientScript/mojofckconfig.js
<add key="FCKeditor:CustomConfigPath" value="~/ClientScript/mojofckconfig.js" />
You could copy and modify that file and then make it use your custom version by putting ths setting in user.config so it will override the setting frm Web.config.
However, if the fonts you specify are not installed on clioent machines it will not work. The ones currently in the list are generally available on most machines.
Also, my recommendation is to never use the font selector in the editor. In fact I'm thinking of removing that by default and make it a config setting if you want to enable it. The reason is, its contrary to the notion of having a skinable site to use hard coded font names. If you use those in your content then those fonts will be used no matter what skin is used. Next year you may make a new skin design and that font may look ugly in your new skin and now you have to fix it by editing all the content to remove that font. Its much better to use css classes so that the fonts are determined by the skin and not hard coded into your content. Same issue with the font size dropdown and font colors, I recommend don't use them at all, in the long run you will regret it. I think at one time I removed those dropdowns but they slipped back in again along the way. I plan to remove them by default in a future release because it encourages bad practices with your content.
Hope it helps,
Joe