I've always been interested in seeing games evolve through their development and inevitably having content cut from them, leading to a wealth of screenshots, videos, interviews, and even music and sound effects that are never seen in the released game.
Unseen64 has some great material on it, I've gone through quite a bit on the site and it always amazes me how is removed before games see the light of day. They also posted the
trailer of Dinosaur Planet on Youtube, which is really quite interesting because it seems like the game was almost complete at that point.
Zelda 64 probably recieved one of the biggest overhauls, since it was originally a 64DD game and was supposed to have all kinds of amazing features that took advantage of it. For example, there was going to be some persistant features if the world: cut a bush or tree, and it would remain cut for the rest of the game. It was also going to be based on an in-game time system where you basically had 7 days to save the world, and the day and night cycles were going to be much more dynamic and have a larger focus in the game. Some of the features were eventually rolled into OoT and Majora's Mask (which got a cut down, 3-day time system), but quite a few were never seen. And noone has been able to quite figure out why there's a fully working and fightable Arwing in the game code of OoT...
Resident Evil "1.5" as it's now come to be known was another big one that even today a lot of fans want to see released. It was basically a more action-oriented version of RE2 that had many things not found in the released version. Speaking of Resident Evil, RE4 is another one that went through so major design changes. The first version of it was eventually turned into Devil May Cry, the second (and possibly third) attempts were never shown, and the second-to-last version was eventually shown and videos of it were released. I think it looks like a perfect fusion between the "classic" RE style and RE4...shame nothing came of it.
As far as Half-life 2 goes, I was pretty disappointed that many of the E3 2003 scenes were drastically altered in the final version, but the leaked alpha of the game probably had virtually nothing to do with it. Almost all of the removals and changes were done because the game was, at that point, so unfinished that nothing really fit together in yet, and they weren't even making major design decisions until well after that point. Anyone else remember the Borealis?
It was the first major part of the game they revealed, the tanker that you would start off in and they talked about it a bunch in early interviews and showed screenshots of it and everything, yet it was cut very early during the game's development (before they even showed the game at E3 2003). The entire part in Episode 2 where they make a reference to how the ship "disappeared without a trace" and such seemed to be a direct joke about how they had suddenly removed it from HL2. The "Raising the Bar" book is a good source to find all kinds of information about how the game changed during it's development.
Oh, and another funny thing: neither of the 2 screenshots on the back of the original retail Half-life 2 box are in the game.
Jam it back in, in the dark.