On the surface, Nabokov's big contract makes him the easy choice to let go. However, I don't see the issue here being the cap hit for this year -- or even next year. Here's the problem:
Nabokov: 2008/2009 $5.25 million cap hit
Toskala: 2008/2009 UFA
Marleau: 2008/2009 UFA
Thornton: 2008/2009 UFA
So, both goalies are roughly the same age, and assuming when healthy, can put up roughly the same stats. If the Sharks internal budget is essentially set for this year -- and I have to think that it would be considering the Vladimir Malakhov transaction -- then Doug Wilson probably has the green light to move either goalie.
The question then becomes, how much will Toskala ultimately be worth? Will he want $5.25 million when he becomes UFA or will he want more? Consider this -- Tomas Vokoun got a four-year extension averaging just under $6 million cap hit and Rick Dipietro's ridiculous contract has a cap hit of $4.25 million per season. Assuming that there is some general level of inflation, it wouldn't be surprising for Toskala to get around $6 million at the end of the 2007/2008 season.
Assuming both goalies are playing to the best of their abilities, keeping Nabokov might actually be the smarter thing to do in the long run. With Nabby, at least Doug Wilson has some certainty in the numbers he will be dealing with when it comes to re-signing both Thornton and Marleau.