Here are 57 iPad compatible fonts:
Academy Engraved LET
Apple Color Emoji
Arial Rounded MT Bold
Bangla Sangam MN
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Devanagari Sangam MN
Gujarati Sangam MN
Hiragino Kaku Gothic ProN
Hiragino Mincho ProN
Kannada Sangam MN
Malayalam Sangam MN
Oriya Sangam MN
Sinhala Sangam MN
Tamil Sangam MN
Telugu Sangam MN
Times New Roman
From iBooks Author Help
There are two ways you can change the fonts in your book with iBooks Author:
The Format bar appears below the toolbar in iBooks Author. If you do not see it, choose Show Format Bar from the View menu.
The Fonts window is also available from the Format menu. Choose Format > Font > Show Fonts.
For best results with iPad, use the Format bar to select fonts; the Format bar's font list includes only fonts that are available on the iPad, so the book should look the same in iBooks Author and in iBooks on the iPad. If you use the Fonts window to select your fonts, all fonts available on your computer will be listed. Selecting a font that is unavailable on the iPad may have inconsistent results when you view the book in iBooks.
For a complete list of fonts available on the iPad, see iOS 5: Font list.
Only the iPad-compatible subset of fonts is shown in iBooks Author
If you look at Format > Show Fonts all fonts on your system are shown, and they can all be used of course.
The font window at the top of iBooks Author does seem to show the iPad subset plus whatever else you may have used at the top.