For a program editing the Game Explorer, or replacing it, I have no idea, sorry. Below is information I have managed to figure out due to interest and little to no fear of digging around even when stuff may break.
The multiple uninstall entries may be because the game itself uses that information from its original installer in some way and cannot use GOG's Inno Setup information, so GOG needed to replicate it even though it's not used for an uninstaller (Windows sees both entries in the registry and gladly lists them both in the Add/Remove Programs or Programs&Features lists).
Regarding multiple Game Explorer entries, Windows Vista and 7 has something called "Legacy Games Detection" that detects games that doesn't originally come with support for the Game Explorer, and games are identified using a unique ID - GOG doesn't supply the same ID as LGD does, so LGD comes to the conclusion that the game hasn't been added to the GE yet. This MAY be fixed with new installers using LGD IDs, but I do not know if that may cause other problems instead. Curiously enough, Baldur's Gate has 3 icons in the GE; two installed by GOG and one from LGD.
As for detecting what icon comes from where; in the registry, go to
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\GameUX\Games
All GOG entries are placed there (as well as some others, so don't go nuts removing everything - always exercise great care to not upset the registry). All GOG games either have a ConfigGDFBinaryPath value containing goggame.dll or doesn't have the value at all.
Those entries NOT having that value are the ones categorised as "Unspecified" on Windows 7 (Vista is a bit more forgiving), thay won't work at all, and can be safely deleted (the whole {345A345-345D-...whatever} key/folder).
The entries detected by LGD does NOT sit in .../Games, but in .../S-1-5-21-something (your internal Windows user ID - you'll have to figure out yourself which one is you if there are different users for the whole family) and has a ConfigGDFBinaryPath value containing GameUXLegacyGDFs.dll - these will probably get re-added if you remove them, so if you're hell-bent on only keeping a single icon per game in your GE, remove the GOG entries for these games.
As to why some of the icons are clickable and some are not (Icewind Dale has two "GOG" icons, though only one works, ditto Baldur's Gate) - edit their Title value, refresh the GE window (press F5, like in your browser), and see which one changes.