Have just a few PC game boxes from the 90s (Duke3D, Carmageddon, GTA and a few others), most of which are in very good condition. May or may not have the game CDs.

Anyone know if I could sell these for more than a few bucks, even without the game CD in some cases?

Well,if you find out let me know as I have the entire contents of all my box brought games and hand me downs.But,realistically there isn't a market that I know of,outside of trying to sell them on EBay.

I don't know about the money you will or won't pull in off such an endeavor, but the fact that people have taken to the likes of Etsy to sell reproductions of old game boxes (granted, a majority are focused on console) suggests that there's a market out there for this type of thing, even if it is a niche one geared toward the hardcore collector crowd.

There is always market for complete games (box, CD, all accompanying material etc.)

Regarding only boxes:
Considering the fact that on Amazon and such, only game discs are being regularly sold without the accompanying material, I'd wager that some of the people that buy them would be looking to complete the package. And considering you have quite popular games like Duke or Carmageddon, I think they would be quite sellable.