It seems to be possible in iOS 5 using the UIAppearance proxy.
[[UILabel appearance] setFont:[UIFont fontWithName:@"YourFontName" size:17.0]];That will set the font to be whatever your custom font is for all UILabels in your app. You'll need to repeat it for each control (UIButton, UILabel, etc.).
Remember you'll need to put the UIAppFonts value in your info.plist and include the name of the font you're including.
http://stackoverflow.com/questions/8707082/set-a-default-font-for-whole-ios-app