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Obvious spoilers:

No matter the end you get, all mass relays are destroyed. Does this mean all the aliens force you got together are stuck in the solar system?

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In the Extended Cut the relays are no longer fully destroyed, only damaged - except for one ending. If Shepard chooses to destroy the Reapers but has a low score, the Charon relay is destroyed.

In all other cases ongoing repairs on the relay are shown. If Shepard chooses to control the Reapers, they are actually shown repairing the relay. Given that they created the relay network it would be quite easy for them to repair the relays.

Also, in the Extended Cut Admiral Hackett gives explicit orders to all ships to retreat before the Crucibleis activated. The allied forces are thus not all stranded directly in the Sol System but possibly near (relatively) by.
As can be seen by the Normandy SR-2 emergency landing/crashing on a jungle planet. It's indicated that Joker waited until the last moment and thus the Normandy SR-2was probably one of the last ships to jump out of the system.

The game gives no indication as to how long the repairs will take, but as the entire network probably needs repairing, it might take a while. Still, I think we can assume that the allied forces are able to go home after a while.

Regarding the worst case scenario, the destruction of the relay:
While standard FTL is shown to allow travel within a star cluster in decent time, the different clusters are much farther apart.
So without the network it would be very difficult if not impossible for each fleet to reach their respective homeworlds. Especially because fuel is not readily avaiable outside of colonized space - which is basically only close to the network. The fleets would have to travel through large parts of unknown space and would have to find fuel there somehow.

It would certainly take a very long time. A generation ship might be able to eventually reach the homeworld, but it would be much more sensible for most of the ships to find a suitable planet and colonize it.

Edit: There is actually a new ending in the Extended Cut, where the relays are also not destroyed. But it's a very different ending, so that the question doesn't really apply to it in my opinion. So it's not included when I said in all other cases above.

Read more about the changes of the Extended Cut in this Wiki entry.

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There won't be a canonical answer until the ending DLC is released, unfortunately, if then.

However, FTL travel is possible without mass relays (at roughly 15 light-years per 24 hours, given sufficient supplies of eezo/He3 and reachable masses to discharge drives into), so they're not completely trapped, no. It's an open question whether they would have enough supplies to return to their home systems from earth. If enough of the Quarian Liveships survived, there would at least be food for the Turians and Quarians; if not, then those two races might have a rough time of it unless there are (or can be built) sufficient dextro-food facilities in Earth or its orbit.

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