The Maria Mystery (Extra)

There is more to the flashbacks, as well what is said during Shadow the Hedgehog levels like "The Doom" and "Lost Impact."

Still, I think I've covered the biggest "mysteries," here (bigger project than I imagined). However if looking for answers solo, here's some videos displaying the matter and a list of her main appearances:

Videos

• Maria's death in the English and Japanese versions of Sonic X. 
• Maria's death including the uncensored beginning of Shadow the Hedgehog
• Clips from Shadow the Hedgehog, Sonic Adventure 2, and Sonic X (Sub)

List Of Appearances

Sonic Adventure 2

There are three flashbacks in Sonic Adventure 2.

• (Team Dark) Shadow and Maria run down one of the halls (Shadow's point of view). Then it skips to Maria's promise.
• (Team Dark) In the second, there is a scene with the two staring out one of the Ark's windows, with Shadow debating his purpose.
• (Last Story) Maria's real promise.

Later, the Professor's diary confirms Maria's death.

Sonic Battle

Mentioned in the Professor's Journals. 

Shadow The Hedgehog

• In the game's first cutscene, Shadow and Maria are chased but this time she's killed in the hall.
• (Semi-Dark) Following the story to "The Doom" will reveal a flashback--when the Ark was taken over. 
• Black Doom shows Shadow the first cutscene but from space (although it's possible they get away). 
• In "The Doom," Shadow has the option to exact revenge on GUN (not likely in the actual event since they hadn't killed Maria yet) to save researchers (Can Shadow say no to Maria?) or to simply escape as soon as possible (most likely scenario).
• The end reveals another flashback with a Gun robot implied to have killed Maria.
• (Hero) If taking the story to "Lost Impact" Shadow will recall an event from before GUN invaded. The Artificial Chaos (from SA2) have gone rouge, and it's up to Shadow to either help stop them or get to the goal.
• Another version of Maria's promise. This one is significantly shorter.
• (Last Way) In the end of the game, Maria appears in a video with Gerald warning Shadow of things to come.

Dark Brotherhood

Mentioned in Codex

Sonic X

There are four major flashbacks in Sonic X.

• (ep 36) Shadow remembers running from the military with Maria and Gerald. Then Maria--despite Shadow's protest--launches him to earth. Shadow also recalls looking out the window with Maria, both wishing to see the planet.
• (ep 37) The next information comes from Mr. Schimtz, who was one of the soldiers on the Ark. He reveals that he fired at her.
• (ep 38) Two final bits are seen in another episode. One is Maria's promise, and the other features Maria wearing a pink dress (the one might simply be a fantasy of them getting to see earth).
• She makes a cameo appearance in flashbacks in season 3. 

Archie Comics

• (issue 98) Maria's first appearance.
• (issue 141) A holographic version of her helps Shadow find his purpose.
• She had a few flashbacks and cameos in other issues.