Anyone have any preference on front and rear pads?

The rear rotor has some scratches on the inside as if a rock got stuck between the pad and rotor.
Will that need to be replaced as well?

I prefer the EBC's.  Some good info here:

http://wiki.gstwins.com/index.php?n=Upgrades.BrakePads

If the scratch is not too deep it will be OK. Even a deep scratch will not affect braking but may be illegal.

On the subject of pads, I swapped my standard rear pads when the bike was still quite new for Vesrah W Organic pads. This was done to stop the constant squealing. The packaging (all in Japanese as they are made in Japan and I bought them in Japan) does not specify rating other than "organic".

It totally changed the feel and performance of the rear brake. Yes. it is sensitive and easier to lock up but it gives fantastic feed-back and I had no trouble with unexpected lock-ups when running flat out on the race track. Extremely hard braking from high speeds had the tyres complaining but there were no surprises. In fact, I was very surprised how hard I could jump on the brakes and still feel comfortable, MUCH harder than I ever have on the road.   

They are definitely much softer/bitier(?) than the original pads, which I still have, and have given the brakes a rear bias but that is fine by me. In my mind, I would rather have a tendency to lock the rear brake than the other way around. Having said that, though, it has only happened twice in three years since I fitted them. In both cases it was unexpected but was more due to poor road surface (gravel) than a braking problem. On dry bitumen it feels fantastic and they are perfectly quiet. 

Macka

I used the EBC organic pads front and rear for over 100k GS miles and liked them for all around use here in NE Ohio but found them not adequate for very hard riding during the mountain years.  Turned the front rotor blue twice completely fading it out once on long fast downhill runs thru the twisties.  Used the EBC HH pads front and rear after that and they were much more powerful than their organics with no fade. 

Discovered the Emgo pads when I needed some front pads locally in a hurry once and found them to be as good as the OEM pads back then and used them front and rear after that for about 50k miles.  More recently I replaced  both the rusty worn out front and rear calipers with very low mileage ones front ebay and they came with Tikico HH front and SBS FF rear pads, a very good combination for the GSs I think but my riding has really slowed down the past couple years.  About time I finally started acting my age.     I think the GSs came with HH front and FF rear pads as oem in recent years since they started marking pads with the friction grade.