Meme Acknowledgment: BioWare merchandising produced shirts for the "Sir Isaac Newton is the deadliest sonofabitch in space!" and "I'm Commander Shepard, and this is my favorite store on the Citadel" memes.
Cut content from the Firewalker DLC reveals that one of the scientists you're trying to find was a minor NPC from the first game on Eden Prime, the one who was "raving".
Unimplemented content, pre-release posts on Weekes's dev blog, and other leaks indicate that Tali, Miranda and Thane could be romanced by Shepards of either gender in earlier development. In the final product, the most visible remainder of this is that most of Tali's lines are the same for both Shepards, which are clearly intended to nudge the player to a romance with her. Female Shepard can even attempt to initiate a romance with Tali, but she will dodge the issue.
Similarly, Kenneth and Gabriella were meant to be romanceable like Kelly.
Character recruitment was originally intended to be much more open-ended, and modding your save file to add party members before you should be able to recruit them will let you hear their dialog for earlier circumstances, such as taking Legion to Purgatory. This likely changed because of the late decision to split the Xbox 360 version of the game into two discs; the forced recruitment progression funnels the player along a path that's not entirely linear, but predictable enough to split the game with.
A few leftover voice recordings in the released game indicated that Liara was initially intended to have a much deeper and longer storyline — which was later made a reality with the DLC Lair of the Shadow Broker.
Early video previews showed more involved gun mechanics; weapons would cool down on their own à la the first game, with ejectable thermal clips as a "need More Dakka right this second" option. Specialized ammunition was shown to be a consumable resource instead of a passive ability and as such could be turned on or off at will.
Going through the dialogue and screen text files reveals that several of the loyalty missions originally had very different plots:
"Bored with being the galaxy's top bounty hunter, Zaeed's also exhausted by up-and-comers seeking a rep written in his blood. Now he's learned that the second-best bounty hunter has gone corporate, and job one is to kill Zaeed. Zaeed's plan: wipe them out first... with extreme prejudice." "You helped Zaeed fake his own death, and he's grateful." "Kasumi revealed that Nava Corp has designed and is about to unleash tailored bio-viruses against the citizens of the Alliance. Only Nava Corp possesses the vaccines. Kasumi needs you to help stop Nava Corp permanently."