I'd hope BioWare would come up with something creative and maybe even symbolic for the deafeat of the reapers. Simply fighting and destroying them, uploading a virus, finding a powerful ancient weapon, or trapping them would all be too easy and cliche' after all that "beyond your comprehension" and "the end of everything" talk. The reapers need to be truly unstoppable by normal means, and their defeat should tie back into the main themes of the series in some way.
If it were me writing the ending, I'd probably go with one of the more winning with a huge sacrifice type of endings. But it needs to be something symbolic that relates to the series main themes such as the blurred lines between organic and synthetic life, and what it truly means to be "alive." As well as the whole paragon/renegade "do the ends justify the means?" conflict.
For example, the paragon ending could involve choosing to fight the reapers to the very end, never giving in and "losing your humanity" to beat them. Ultimately the ending means the death of both the reapers and all the galaxy's inhabitants. The reasoning being that organic life will supposedly always replinish itself naturally (I guess evolution, not saying I believe in evolution or not, just saying that would sort of be the idea and the series has played with the concept a bit already) and therefore organic life will always endure longer than synthetic life because of this, making Sovereign's statement "we are the pinnacle of evolution" ironically false. Organic life itself will always be the "pinnacle", if you get what I mean. So this is the truly selfless paragon ending - you save the galaxy by paving the way for future species to live in freedom, but at the cost of everything and everyone you've ever known. Alternatively, from a religious or more specifically theism standpoint (again, I'm making no statements about my own views), instead of evolutionary one; you could still use the same concept and have Shepard sacrific everything, sort of like The Flood, only there is no Ark, instead, everything resets because of the sacrifice made, and God basically starts over. I guess you could say this was the rapture. They could write this ending in a way that it neither definitely supports either side (evolution vs. creationism) as to not be too controversial, the idea that you sacrifice everything for the sake of new future generations to live in freedom works either way.
And in the renegade ending, Shepard chooses to keep everything and everyone intact, but at the cost of all of their "humanity" (or "organicy" yes, I made up that word since I'm not exclusively talking about humans, aliens are included) by submitting to the reapers and becoming a sort of synthetic-organic hybrid just like the reapers are revielled to be in ME2, and what Saren was planning to do in ME1. So the entire galaxy becomes ignorant slaves with no thoughts of their own, indoctrinated to believe the reapers brought peace and happyness (ironic because happyness is an emotion to the reapers and it is questionable if any of them are still "alive." This also establishes a cycle for any new species to rise up naturally in the galaxy as they are all immediately enslaved and turned into synthetic-organic hybrids and integrated into the new galactic order of almost-mindless husks. As a cool chilling last scene, it could show a machine-Shepard following in line emotionlessly as an unknowing slave, then for just one second you see him give a look of sadness and regret... before going right back to his duties.