Control:
The Heart of the Janus Base was SWARMING with Janus Operatives, especially near the computer where Natalya worked, which wasn't on the bottom floor like in the game.
If you kill Boris in the game, Natalya will get mad and run away.  In the movie she hits him.
The control center has other computer programmers in the movie.
Whatever happened to the revolving pen of Boris's?  In the movie it was Boris's only main thing.
In the game you have to just let Boris go, but in the movie, he is to be frozen in liquid nitrogen.

Caverns:
There were never any Subterranean Water Caverns.
There was a large scene of James and Natalya searching the immediate areas of Cuba where they were told the antenna was. They did not get there by elevator, eliminating the Caverns, since there were none.  They were in a plane at the time, and they searched until the lake emptied and there it [the Cradle] was.

Cradle:
Bond didn't "throw a wrench in the works" in the game, which prevented GoldenEye realignment.
Trevelyan didn't realign the GoldenEye, Boris was having enough trouble doing that.  Alec was busy trying to kill Bond.
During the Cradle fight, the only weapons available during the battle was a KF7 and Alec's Beretta.
Trevelyan was thrown off the cradle, not shot off.
Alec tried to kill Bond. The other Janus Operatives were in the midst of the explosions in the Control Center.
Bond went down the ladder before Trevelyan did.
Natalya saved Bond when she held up the helicopter pilot, which was in the middle of the Trevelyan fight.  The helicopter is nowhere to be seen until you defeat Alec.
At the end of the movie the Marines pop up as Bond and Natalya are kissing.
In the cradle Bond rides a lift to the top.
Natalya came up with Bond, while in the game he's alone, and there's no elevator.  She acts dead so the guard would come and investigate, allowing Bond to drop on him.
The cradle falls down on the control room in the end.
Trevelyan doesn't automatically die from falling off the cradle.  Instead, the cradle falls on him.

Aztec:
The Aztec stage is a continuation of sorts of the Moonraker Bond flick, and the deal is that the Drax Corporation still exists.  Bond's task is to reprogram their next unauthorized shuttle launch so MI6 can recapture it and see what's up.
Teotihuac?n was actually a Toltec city, not Aztec.
In Moonraker the lasers were semi-automatic and fired one beam at a time, and were also larger.  In the game the laser is smaller and is an automatic like the taser.

Egyptian:
The Egyptian Temple in el-Saghira is where the Golden Gun resides, and where the presumed-dead Baron Samedi has challenged Bond to a duel to the death.  The gun is from The Man With the Golden Gun (duh), where Bond fought Scaramanga, while Samedi, a sorcerer, battled with 007 in Live and Let Die.
According to "The Ultimate James Bond Dossier" (a CD-Rom which is official) the Golden Gun is stored at Q's Lab (I don't know how either, so don't ask).  However, the background info says "the whereabouts were unknown".
Neither Scaramanga nor Baron Samedi were ever anywhere near Egypt.  Scaramanga was located near Hong Kong in
The Man with the Golden Gun.  Samedi was in the Carribean.