Tonight I was playing Black Tower (BLACKTWR.WAD, Master Levels) and noticed an occlusion error in the "top" of the tower where you fight the Cyberdemon. The rooms holding the monsters that teleport into the playable area of the map are visible beyond the edge of the tower with the OpenGL renderer. This does not happen in software.
Additionally, I've included some screenshots of E4M6 which I posted on Doomworld a while back. The secret area with the plasma gun looks to have a similar issue, where its walls are visible in OpenGL but aren't in software. E4M6 has another issue where areas are occluded behind the lowered sky sector that shouldn't be, also, and a texture offseting issue.
In all of these cases, GZDoom's GL renderer draws these areas in the same way as software.