49 is correct!

43 is not.

43.  a) This entry in the series can be seen as connected to the first entry in a variety of ways.
b) One way this game is connected to the first entry is that they have the same final boss.

42.  This was the first video game to have credits, but they were put in there without the publisher knowing.

41.  The premise to this game is the same as the Neverending Story, which is ironic, since this is a spinoff of a series that has the opposite meaning.

42: Adventure?

Incorrect, though a pretty good guess. This is indeed a Star Wars game, and Shadows of the Empire does have a variety of styles come to think of it. But I'm looking for another one. Side-hint, if the 3rd hint is unclear, while my game has a decent amount of variety through the levels, it does always stay on-rails, and never has free-roaming like SotE, not even on the first person shooter level.

Still no correct guesses for these two, so here's the next hint for both.

#37

-"You think there's a dog buried in this."

-"I can tell you're not a yesterday's grouse's son."

-"You need to fix it before old twig-pants inside the plant has a shit fit."

-The above are all Finnish language idioms translated essentially word for word and said in the game by the janitor.

#36

-Make it to the spring of the third year to meet the person who started you on this journey

-The person you're meeting is your grandfather

-Well, the ghost of your grandfather

-The game started with you inheriting your grandfather's old farm

41. Super Mario Land.
Another of the first games I can remember playing, but unlike Link's Awakening, I could never beat this game. I would make it as far level 9 or even 10 , then run out of lives and have to return to the beginning. It wasn't until I returned to the game as a teenager that I finally beat it. This pick is probably due to nostalgia more than any other item on my list as the game is not that great overall, but it's still got a special spot in my heart regardless and I replay it about once a year.

Correct.

Here are some more clues to my games:

43.  a) This entry in the series can be seen as connected to the first entry in a variety of ways.
b) One way this game is connected to the first entry is that they have the same final boss.
c) One way this game is connected to the first entry is that they both have an overworld with much of it open for you to explore from the beginning.

41.  a) The premise to this game is the same as the Neverending Story, which is ironic, since this is a spinoff of a series that has the opposite meaning.
b)  This is a Gameboy Advance title.

40.  The source material for this game is classic Chinese literature, but it is not any of the games from the "3 Kingdoms" era.  First in the series.

39.  One of the voice actors in the English version of this game also sees dead people.  First in the series.

#41 The Original likely inspired by

I feel like I'm getting deja-vu here - maybe this stumped me last year too.

Rebel Assault?

Could be. Rebel Assault, the second game to be exact, is correct though.