It is simple to tell them apart visually: the Exige is the hardtop, and the Elise is the open top.
There are more internal differences, and I believe that the Exige isn't in production any more. (Could be wrong here...)
If you go the the Lotus UK site: http://www.lotuscars.co.uk
Then click on "CARS" (top left of the screen), then click on "The Cars" on the LEFT side of the screen, then click "Models" (also on the LEFT) side of the screen, you can compare the Exige to the other models.
They are very lovely cars... but I think I would miss the open air experience of the Elise.
Quite a few differences, most of which were aimed at making the exige good on the track..
both the clams are different (the front clam is a lot wider: it has ducting behind the wheelarch for brake cooling, the rear clam has a roof on, as well as ducts and scoops for various reasons)
the engines on offer were different (more power/less reliability);
there's currently no S2 exige (though one is rumoured),
the exige has a big rear wing,
bigger wheels (only black alloys)
built-in race-style harnesses and harnessbar
built-on fire extinguisher
As far as I know you can't get exiges any more. There *might* be an S2 or S3 exige but that's just speculation.
The front clam shouldn't be much of a challenge after they have done the S2 road car. I agree the rear clam will be difficult.
All I've heard is a rumour that an S2 exige is under development, not where it will be sold... but the US is going to be an important market for Lotus and I'd be surprised if they don't go ahead and sell it there.