I wasn't sure of this myself until i did a bit of testing...
The Back/Forward buttons are for PDFs with a Table Of Contents. If you have a multi-page PDF with a TOC open it up in Preview. Go to a page towards the middle of the document from the TOC in the Drawer (I'll use page 30 for the heck of it) . Now go to page 4. Click the back button. It should take you back to page 30. Actually, you'll notice that the Back/Forward buttons were inactive until you went to page 30 (at which point the Back button activates, then when you go to page 4 the Forward button activates).
I'm sure you can see how this differs from Page Up/Down.
cheers
edit: heh, funny bug. I opened a 338 page PDF. Obviously, it opens to page one. I clicked on a link in the TOC which took me to page 124. I hit the Back button and it took me to... page 2?! Goofy.