the apple case does not come with a screen protector. in fact, apple recently banned all screen protector films from their stores. so don't go looking for one there. one of the web sites (engadget? gizmodo? i forgot) did a scratch test with a nail. they said it didn't leave a mark on the glass, but scratched up the aluminum back pretty easily.
personally i like a screen protector not for the scratch protection, but i like the feel of the film verses the glass. that's just a personal preference.
not all screen films are alike either. some are just vinyl, some are various forms of hard plastic or rubber. my personal favorite is the 3M film that was originally developed for helicopter blades (or so they claim). both zagg.com and bestkinsever.com sell the stuff, with the latter being generally half the price. decalgirl.com also sells screen protectors along with skins for the back, though i'm not sure what material they use. i have one of their skins on my 600 and it appears to be a printed vinyl material. good protection from scratches but not against dropping.
it boils down to this:
a naked ipad seems well protected from screen scratches, but not so good on the back. setting your ipod down on a table, or worse yet, a concrete bench, is likely to leave some marks.
screen films can protect the glass surface but provide a different "feel" on your finger. they can also make it less glossy (and reflective) depending on the material it is made from.
a film or skin for the back surface can provide scratch protection, but won't save you from a drop of any distance. it will also protect your ipad when in a backpack or bag from scratches from other objects.
sleeves made out of neoprene provide good light protection when your ipad is in it, but obviously none when it is out of it. might help survive a drop on a carpet, or onto a table from a low height above it. good protection when your ipad is in your backpack or bag as well from other objects. apple's case isn't neoprene but it falls into this category as well, but also lets you use the ipad still in the case.
for serious drop protection, you're going to need a large, bulky case with some padding. expect it to be significantly larger than your ipad to provide any sort of decent protection. it's unlikely you're going to be able to use your ipad when in such a container as well, and it will probably be too large to fit into a backpack or bag.
timbuk2.com has a variety of bags and backpacks for laptops and other devices. not necessarily cheap, but they are very good quality. i've been using a messenger bag of theirs for well over a year that has gone around the world several times with me and looks a day old. it's stuffed with a 15" laptop, assorted gear, cords, chargers, a camera, papers, and now my ipad (which replaces my sony 600 which used to travel with me). it has a padded compartment for my laptop, but not my ipad.