I'm thinkin he will pull it off in an "Independence Day" fashion.
Heres what I mean by that:

If you remember the movie Independence Day, American Hero's Will Smith and Jeff Goldblum fly up to space and destroy the alien mothership making all the other invading ships much weaker and thus eventually destroyed by the military.  I have a feeling there will basically be a "Mother-Reaper" (possibly Harbinger) that Shepard will have to destroy and this would cause either 1) All other reapers to simply de-activate/blow the hell up or    2) make them substantially weaker than they previously were making it much easier to fight against them

Again just my theory because I really can't think of any other solution since it took an entire fleet to destroy just one reaper and now there are thousands or millions of them

Would also like to add that I would like it to be more "creative" than this but it seems quite possible

Dude no. Don't be stupid. It'll be a dance-off. Each of your party members goes against an individual Reaper and their success depends on their loyalty to you.

Here's my theory

Well, let's hope that it doesn't play out that way.

IT's the only possible way it'd end don't you think?

I doubt Bioware want an ending to their epic trilogy that people can look at and say "Hey, that was a bit like independence Day."

" Here's my theory

SPOILER WARNING: Click here to reveal hidden content.

Explosions will be involved. 

"

Yes, but your wrong in the details.

Jack gets angry and blows up the Chan- I mean the Citadel.

" @MariachiMacabre: Fuck you and your theory. I'll only be 100% on board once Bioware announces DDR dance mats bundled with ME 3 copies. "

You're wrong. Shepard will have to stick his cacacho in their piddydiddly and make them wakawaka... and then they blow up.

Shepard goes back in time to get the Warden and Hawke to bust a cap in Harbinger's ass.  After the credits are finished and your sent back to the main menu the title changes to Dragon Age 3 and the trilogy is complete.

Mars will have a dues ex machina on the prothean site

Jeff Goldblum has a harem of Asari.

Well since there is that Ogre figure in Mass Effect 2, doesn't that mean that DA and ME are both in the same universe?

He'll shoot at a really stupid looking robot until it dies.

So Randy Quaid voice acting confirmed? 

Roundhouse kick. The only way to end any epic story.

I predict a surprise downbeat ending, where the reapers sneak-up on him while he's mining a planet for made-up-element #45 or trying to fuck an alien.

" Well since there is that Ogre figure in Mass Effect 2, doesn't that mean that DA and ME are both in the same universe?

Thus my theory is that Sandal is involved.

"

He'll shoot at glowing weak spots until they all die.

" @Afroman269 said:

" Here's my theory

SPOILER WARNING: Click here to reveal hidden content.

Explosions will be involved. 

"

Another stupid and baseless theory. How would dancing cause explosions? "

I@MariachiMacabre said:

" Dude no. Don't be stupid. It'll be a dance-off. Each of your party members goes against an individual Reaper and their success depends on their loyalty to you. "

He wont beat the reapers he will die around the middle of the game and for the rest of the game you have to play as the illusive man

Alternatively, they could reconfigure the Mass Relays so that they function as mass accelerator cannons that have a range of a galactic spiral arm.

Shepard eventually finds the Star Wars Galaxy, and helps destroy the Third Death Star. In turn, he is granted a lightsaber and is taught the force, which he uses to destroy the Harbinger ship.

I can see an Independence Day-esque ending destroying the Mother Reaper weakening all the other reapers and by that time you will have the geth on your side. the humans, geth, quarians, turians, asari, krogan, salarians, rachni, and keepers, and possibly a surprise prothean  will assault the remaining reapers destroying them all and the galaxy lives happily ever after.

" Here's my theory

SPOILER WARNING: Click here to reveal hidden content.

Explosions will be involved. 

"

My theory is that they'll pull something out of their asses.

Conrad Verner will show up and idiotically kill the reapers by accident.

He's probably going to have to do something to a relay to block them entirely, that or re-program them for farming initiatives....

So Shepard is going to punch a reaper in the face and shout 'welcome to earth' at it? Like the movie right?

Quoting this following post on YouTube:

I think Shepard will inadvertently trip over some sort of wire that will cause him/her to fire his/her gun into some crucial piece of machinery  that will cause a Rube Goldbergian style chain of events that ultimately leads to the destruction of the Reaper fleet.  This music will be playing as it happens:
  

I don't think Shepard actually will defeat the Reapers. I believe Shepard is going to die once and for all in some sort of last stand and the Reaper cycle will finally continue. It just feels like he (or she) will die this time.

Yes, but your wrong in the details.

They will be defeated when Goldblum, who is totally available as a party member in ME3, uploads a computer virus into harbinger, thus causing them to shutdown.

Will Smith and Jeff Goldblum confirmed as Mass Effect 3 squad members?

Will Smith and Jeff Goldblum confirmed as Mass Effect 3 squad members?

With a high enough Paragon or Renegade score Shepard will persuade the Reapers to leave via an intense and dramatic conversation.

During Tali's recruitment mission they talk about a sun that has gone prematurely red giant due to dark energy. I will bet Shepard will have to turn Sol into a super nova to destroy the reapers as well as earth.

Oh.. I thought youmeant he was going to fly up their corn hole.

I think he will punch them to death.

Shepard BECOMES A REAPER and kills them from the inside.  In a tragic ending, Shepard dies in the end, but humanity surivives..  Blah, blah, blah, human spirit..etc.