Unfortunatly there is some speculation as to whether there will be a sequel.
The head writer Ragnar Tørnquist seems to be very involved in getting Funcom's latest offering The Secret World MMO developed and launched.
He has however indicated that an episodic format of Dreamfall Chapters is floating around at Funcom.
I enclose an excerpt of what he said as his blog seems to be down to link to: Nothing major is currently happening on Dreamfall Chapters.
The people who will be involved when it does happen – myself included – are tied up in other projects, primarily The Secret World.
TSW will continue to be my (and their) primary focus for a while longer…but that doesn’t mean nothing at all is happening with Chapters.
It just means that it’s not (at least not officially) in production – for now.
gaming.stackexchange.com/users/776/Tornal
Yes, there's at least one hint to the fate of April in The Longest Journey.
While it's never explicitly stated, but Lady Alvane , (the mysterious old woman who tells the story) appears to be April herself.
At least if you take into account that she knows the story of April very detailed and that Crow is with her, and as it seems he was for a longer time as he asks "You don't plan to go on an adventure again, do you?"
(or similar) at the end of The Longest Journey.
gaming.stackexchange.com/users/1716/Bobby
Lady Alvane could also be Zoe:
Remember how she says at the very end of TLJ that it had been a long time since she remembered "April Ryan"?
Unless she is refering go herself in third person, it could be that it's someone else, talking about april.
Remember how Crow tells Zoe "From now on, I'll be your sidekick" after both of them are mad at april for not wanted to help them out?
In that last scene from TLJ
we see him in Lady Alvanes house.
gaming.stackexchange.com/users/24002/bubu
It's a cliffhanger.
They're planning to do a sequel, so the characters can't all be dead/incapacitated.
I'm guessing at least Zoe is going to come out of the coma somehow and April might not be completely dead after all.
According to wikipedia work on the sequel has not (yet?)
begun, so there's nothing definitive on the fate of the characters.
gaming.stackexchange.com/users/605/sepp2k
As of the 21st of October a sequel has been published named 'Dreamfall Chapters', in which it is clear from the first minutes what happened to Zoe and April.
April died.
Her body burned in a burial ritual reminiscing that of a viking burial ritual, yet more magical.
Zoe has been in a comatose state ever since the incident and you join her side again after 12 months has passed.
gaming.stackexchange.com/users/90554/Scribbd
Technically the following count as out of game hints, but they do clarify the in game occurances at the end of Dreamfall.
I also include this info here because some of the other answers are now out of date.
Dreamfall: Chapters , the sequel to Dreamfall, has been funded via Kickstarter and is in development.
The Kickstarter description indicates that while it focuses on wrapping up Zoe's story, it is also a continuation of April's story wherein we learn her destiny.
It also notes that April was "fatally wounded" at the end of Dreamfall, which presumably means she will not be dead at the start of Chapters.
As a further OOC hint, Red Thread tried unsuccessfully to raise enough extra money to start work on The Longest Journey home which concludes April's story.
This also strongly implies April will survive Dreamfall and Chapters.
So, Zoe is definitely in a coma, and April is fatally wounded but not dead yet.
However, both their stories will continue in Dreamfall:
Chapters and possibly The Longest Journey Home.
So things are either not as they seem, or more plausibly, likely to change quickly within Dreamfall: Chapters.
gaming.stackexchange.com/users/8490/Christi
At the end of Dreamfall, April Ryan  (spoilers hidden)    appears to have been killed, and Zoe is in a coma.   Are there any hints throughout the game that their fate is really different than what it appears to be on the surface?
At the end of Dreamfall, what is the fate of April Ryan and Zoe Castillo?
gaming.stackexchange.com
<dreamfall-the-longest-journey>
gaming.stackexchange.com/questions/115
gaming.stackexchange.com/users/11/Jeffrey
Lady Alvane could be April or Zoe. They are planning a sequel so the characters can't all be dead. It's a cliffhanger. Although it has never explicitly stated, there is speculation that Lady Alvane may be April herself. Lady Alvane could also be Zoe. A sequel has been published named 'Dreamfall Chapters', in which it is clear from the first few minutes what has happened to Zoe and April.  It seems that Zoe is definitely in a coma, and April is fatally wounded but not dead yet.  
Although it has never explicitly stated, there is speculation that Lady Alvane may be April herself. Lady Alvane could also be Zoe. It's a cliffhanger. A sequel is planned, so the characters can't all be dead or incapacitated. A sequel has been published named 'Dreamfall Chapters', in which it is clear from the first few minutes what has happened to Zoe and April.  It seems that Zoe is definitely in a coma, and April is fatally wounded but not dead yet.  