Day 1
Not sure what the cause is, but having some problems with my GS500E today. While in 3rd gear at around 5000 rpm, the engine stopped responding to my throttle and kind of just fluctuated at 5000 for a while. At the same time, either the carbs or the exhaust was backfiring, and I ended up having to hit the engine cutoff switch and pulling to the side. I couldn't start it back up, but after about 5 minutes or so, the bike would start again. The whole process ended up happening 2 more times on my way home; I'd get around 5-10 minutes on the bike and then the problem would pop up again. Also, one time when I didn't hit the cutoff switch and brought the bike to a stop with the clutch pulled in, the engine died.

Day 2
I took it to Suzuki of Oakland today to have it looked at. They cleaned and synched the carbs, cleaned the air filter, plugged a vacuum leak in both carbs, andd did a compression check in both cylinders. On the way back home on 880 though (dunno if any of you saw me, but I was the one that was on the shoulder), the bike had the same problems as before. I was at around 6k RPM, when the engine pretty much just died. Happened 3 more times within 2 minutes of each other. The problem then just disappeared, and I made it back the last 15 minutes without any problems. So now I have no idea what else the problem could be, so they're picking it up tomorrow and bringing it back to the dealership to take a look at.

O also, after it happens, the bike wont start up for like 2 or 3 minutes, but then fires up fine. Also, when the engine stops responding/dies, i hear a pop-pop-pop sound, I think from the exhaust because it sounds like its coming from my right side. At the same time, the engine loses power but then regains it and then loses it again and regains it, causing the bike to lurch back and forth.

Day 5
Shop took another look at it and checked out the tank and blew out all the hoses, but couldn't reproduce the problem. It's kinda weird how the problem happens pretty randomly, but hopefully it's gone now.

Anyone have any other ideas as to what it could have been?

Are all your gaskets in good condition - ie on the exhaust no holes, carbs etc..

Maybe you are loosing a cylinder on one side. If it happens again stop and pull out one spark plug cap and see what happens.

If it happens again, before attempting to start, open the fuel lid slowly and try to listen for a sucking sound. Maybe your vent isn't working and you are starving your carbs with vac lock?

A wild guess, but cheap to check.

Try putting the petcock on Prime when it happens.

Also try searching for fuel starvation

This actually did happen to me. The mechanics failed to open the fuel chicken properly after taking off the tank.

My GS has a screwdriver actuated "on-off" at the back of the fuel chicken. You will need a long, flat head screwdriver. Lift the tank slightly, and looking from the right side of the bike, make sure the fuel chicken is fully "on".

My bike used to die suddenly, always at speed. Turns out the tap was half way turned on only and the bike was starving of fuel. Hope this helps.

Yea man, sounds like a classic case of GS fuel starvation.  It's caused by a failure of the vacuum-actuated diaphragm in the frame petcock.  The diaphragm stops opening fully, restricting the flow of gas to the carbs.  The bike runs fine until the carb bowls are empty and then dies when they don't refill fast enough. 

Try running the bike in Prime, which bypasses the diaphragm.  If this fixes your problem look into replacing the petcock with a new factory unit or an aftermarket, non-vacuum operated, model. 

Hm, looks like I'll have to check the tank out some time. Rode it around for 25 miles today and had no problems, but didn't get to reach highway speeds yet so we'll see how it holds out. Looks like it's a fairly common problem, so I guess I'll check it out when I get a hold of some tools. Never worked on a bike before, so wish me luck