If Urdnot Wrex is in Shepard's team and Shepard speaks to General Septimus in Chora's Den, Wrex makes the comment: "How did your kind ever defeat us?" to which Septimus replies "I may be drunk, Krogan, but you're ugly. And tomorrow I'll be sober." This is a reference to a phrase allegedly spoken by Sir Winston Churchill to Bessie Braddock when she accused him of being drunk.
When landing on Earth's moon one can find the wreckage of a probe called "CCCP Luna 23". The Luna 23 is a USSR probe, which was sent to the moon in 1974 to bring rock samples back to Earth. It was damaged during it's landing and stranded on the surface.
When the player destroys the final component of the rogue VI (Virtual Intelligence) on Luna, there is a block of binary displayed as the last gasp of the dying VI. The binary displayed is 01001000 01000101 01001100 01010000 which when translated to ASCI reads "help".
The Legendary Edition of the game will feature multiple changes to the game including: better Mako control, refined combat to feel more like Mass Effect 2 and 3, more character customization, a recreation to the original default Female Shepard to look like the Canon face in 3, and upscaled graphics in the Unreal 3 engine with AI assitance then touched up by hand. This game will recieve the most overhauling in comparison to Mass Effect 2 and 3.
Easter egg: the code to access the neutron purge in the hot labs on Noveria is the same as the transporter coordinates given to the Enterprise in the original series Star Trek episode "The Mark of Gideon." Since this is a nine-digit number it is extremely unlikely to be coincidence.