You mean for text in the template or for the logo? We provide a mechanism to switch between some web-friendly font sets in the template parameters. Regarding the logo, you can use whatever you have installed, no requirements.
Yes, you can specify them for any area by using font-family: fontname; in your css. There are a limited amount of web friendly fonts so if the font you would like to use is not included then you will need to implement something similar to sIFR or FLIR on your site.