I have the exact same problem with my Corolla. Mine is also a 1997. I searched the web and came across this posting from RICorolla. I tried some spray silicone on the channels in the door frame with no success. But, I did find the problem and fixed it, it didn't take long and only cost a couple of bucks.
The noise is coming from a wheel that rides along the track when the window is raised or lowered. It needs to be greased so you have to take the door panel off. This is not difficult. Gently tug on the outer edges of the panel to loosen. There is one screw for the door handle and two more for the behind the armrest. You'll have to pry off the pad on the top of the armrest to get to those screws. There is also one black plastic pushpin-type (like a pop rivet) on the rear of the door. When all of the perimeter is loose, unscrew the four screws on the backside of the panel if it has power windows and feed the switch through the hole in the panel and let it hang. If your's has manual windows, you'll have to remove the window crank. The door handle and trim takes some effort to remove. The back of the handle will reveal hooks that clip into the door frame (you'll see it when it's removed). To remove the handle and trim, lift one edge and then pull it forward. When it's loosened, you can turn the handle 90 degrees and feed it through the hole in the door panel. You do not need to remove that retaining clip regardless of what other sites recommend. I didn't have to. Just let the handle hang in place. By now, the door panel should be removed and frame should be exposed.
At the hole at the bottom of door frame, cut the plastic on three sides with a razor. Make the cut larger than the hole in the door so when you tape it back together, you'll have the door frame as a firm backing when retaping the pieces. (I didn't do that with the first one as shown in pic.) With the window in the lowered position, you'll have easy access to the wheel and track that need to be greased. I used white lithium grease but you can use any all purpose grease. Spread the grease liberally along the track and the outer edges that come in contact with the wheel. Raise the window slightly to get access to where the wheel was just positioned. The grease will not come in contact with the window nor will it be seen when everything is put back together so don't skimp on the grease.
It's been a year and a half since you posted RICorolla. I hope you receive this and it's helpful for you too.
keywords: squeal, screech, squeak, scratch, noise, loud, window
They don't do it in the rain. And no I don't open them in the rain. 
