For some applications on my system, eg: K3B, Scribus and QCad, have overly sized fonts unlike the rest of my system.

Here is a picture:
http://failnation.com/upload/ubr_uploads/snapshot3.png

They do not follow the fonts I set in the system settings dialog like other applications. Any ideas? The one thing these applications have in common is that they are Qt3 I think. Perhaps it's something to do with the default Qt font?

Looking forward to a solution

Since these applications are Qt3, they may not obey the settings that have been set through System Settings. try using KControl from KDE 3 to apply your desired settings.

Turns out that it's a bit heavy on the dependencies to install KControl 3.x. So I managed to fix this by looking at this website:
http://en.gentoo-wiki.com/wiki/Toolkit_Beautification
... and also running /usr/qt/3/bin/qtconfig - turns out the issue was with Qt3 fonts. Thanks a lot!