Font settings are stored in the file gui.ini which can be found in the installation directory (edit: if using win xp, for vista/win7 the appdata dir, check the link below for details). Here are the descriptions that I managed to find or figure out, mostly taken from: http://forums.longestjourney.com/showthread.php?p=83228
bigfont = conversation text, intro text, buttons (yes/no)
smallfont = tooltips
font0 = ? (maybe chapter titles?)
font1 = ?
font2 = copyright text in startup screen
font3 = savegame description, (some) menu headings
font4 = menu items
font5 = conversation log
font6 = diary
font7 = books in the library
The original bigfont used for conversations in the 4disc version was slurry, size 19 (I own it so I checked), so if you want to try it simply delete florentine script and type Slurry in the gui.ini file.
I encourage everyone who has played or will play with the gui.ini file to post their most satisfying choices! The changes have to be made in the first part - [Western].
As for me, the most problematic fonts were bigfont and especially font6 aka the diary which is simply unreadable with the default config. I changed bigfont to tahoma, size 17 and the diary font to garamond (used for tooltips in the default setting) with the default size (15). Garamond works very well as the bigfont too, and when used for the diary it makes it readable while still retaining a certain charm. Monotype corsiva looks ok with the diary too, but you have to make it slightly bigger than the default 15. When i picked the size I made sure that the distribution of words per row is the same or very, very close to the default one, in order not to have any problems later (with monotype corsiva the size should be 16 for font6). I also used tahoma with the default size(12) for tooltips (smallfont). I got the idea for the tahoma font here http://forums.longestjourney.com/showthread.php?t=1520, but his choices were too small for my eyes. I'm using 1280x1024 and 1280x800.
edit: the books in the library are unreadable with the default setting "Florentine Script", I'll probably keep Garamond, 14. As with the diary, Monotype Corsiva works well too (for those who want/need more immersion), but it has to be made bigger (in my case 15, it takes more space than florentine script 13, so it might be problematic at some point, but not necessarily ).
UPDATE: I finished the game some time ago, the diary and books fonts can safely be made bigger. I attached a screenie which is somewhere from the beginning of the game so it won't be a big spoiler, and which shows what's the biggest amount of space used in the diary (vertically). If you wish you can adjust it accordingly. Sometimes the text is denser but it doesn't go over the last row in the screenie, at least with my settings. It shouldn't be too different with different fonts. Btw, the text in the screenie looks blurry due to jpg compression, it's crisp in-game. No screenies for books because of spoilers, but if I remember correctly the max space that the text used with my settings was ~1/2 of the page.
Here's my final gui.ini for those who want to use my settings:
font0 = Folkard™
fontsize0 = 20
font1 = Folkard™
fontsize1 = 12
font2 = Arial
fontsize2 = 14
font3 = Bradley Hand ITC
fontsize3 = 16
font4 = Bradley Hand ITC
fontsize4 = 20
font5 = Bradley Hand ITC
fontsize5 = 16
font6 = Garamond
fontsize6 = 15
font7 = Garamond
fontsize7 = 14