Borderlands is another fresh innovative game. Dead Space is a series that has managed to avoid copying CoD. Even though I didn't care for Red Dead Redemption it was something different as well. Those are the only games I can think of to add to your list.
I don't think borderlands was. The only new thing it did was graphically, but even the whole cartoony thing had been done before. If you don't think the monotonous get a quest, kill x number of mobs, or collect x number of items, or use item x on item y, then return, get a reward, rinse and repeat has been done before, you haven't played many games, because you have essentially just summarised every single MMO ever. Then the combat system is just an fps crossed with an mmo, basically just showing you the numbers rather than hiding them in the background.
I would say it is different, but not inovative, after all nobody is trying to use their formula, or even wants to, because it was executed so damn badly, it was so boring and monotonous, you had 1 hub for most of the game, there were 4 weapons, all were just reskinned with different numbers, but every single one had the same base design and the same animations when fired, the vehicles drove badly, the AI was pretty awful, all of the landscape looked the exact same and was bland. After playing for an hour or two, it got so boring.
Red Dead Redemption is just GTA in the wild west, the formula for it is not innovative, it has been done before. To say it is new and fresh is to say Mafia 2 is also new and fresh "because it is set in the 40's with the mob", when it is clearly still just GTA. That doesn't stop either from being good games, but they brought nothing new.
Dead Space, I can't comment on really because I have only played about half an hour of the first, however it didn't do anything to make the scary environments all that scary because you saw everything. It made you jump, but not scared.
That is a good point though, as it bring about another excellent, innovative game - Amnesia: The Dark Descent.
Portal was special because the level designs were small, yet extremely complex because of the puzzles, puzzles which didn't get repetative, were fresh and challenging when you encountered them, and although at times you would feel you didn't have a clue what to do, everything felt doable, and you knew the answer was staring you in the face so spurred you on. The script was extremely witty and dry, and everything from the timing of the script to the voice acting was done perfectly, but the most important thing was the portal gun. It put you in a perspective of an fps, but you had no lethal weapon, so what were you to do? There were, and still are, no other games in that format, yet it is universally praised.
Minecraft, although similar to Infiminer, is a complete sandbox, allows so much to be built and it really is a complete imagination game. It took the flaws of Infiminer and got rid of them. The fact it is still in beta, yet Notch and the rest of the Mojang devs/artists and millionaires, and that there have already been direct copies created (most notably Fortresscraft) is testament to that.
CoD though is just a backwards step if anything. None of their games are new or fresh, you may as well just play CoD4 with some mods on, because that is essentially what all of the games after it were, they brought nothing new sounds or gameplay wise and graphically it is the same, so why make a full new game? The sooner it crawls into a corner and dies, the better