This was already covered to some extent in Conversion of Fortran 77 code to C++, but I'll take a stab at it here.
I think there's a lot of time wasted translating legacy code to new languages. It takes a phenomenal amount of time and energy to do, and you introduce new bugs when you do it.
Joel mentioned why rewriting from scratch is a horrible idea in Things you Should Never do Part I, and though I realize that translating something to a new language isn't quite the same as rewriting from scratch, I claim it's close enough:
Automated translation tools aren't wonderful because you don't get anything maintainable out of them. You pretty much have to know the old code to understand the new code, and then what have you gained?
To port something manually, you have to know how the code works to do it well. Rewriting code is seldom done by the original developers, so you seldom get people who understand everything that's going on to do the rewrite. I worked at a company where an outsource team was hired to translate an entire website backend from ColdFusion to JSP. That project kept getting delayed and delayed because the port team didn't know the code at all. Our guys never quite liked their design, and they never quite got it right, so there was constant iteration as everyone worked out all the issues that were solved in the original code. Then, the porting itself took forever.
You also need to be familiar with really technical inconsistencies between languages. People who are very familiar with two languages are rare.
For Fortran specifically, I now work at a place where there are millions of lines of legacy Fortran code, and no one here is about to rewrite it. There's just too much risk. Old bugs would have to be re-fixed, and there are hundreds of man-years that went into working out the math. Nobody wants to introduce those kinds of bugs, and it's probably downright unsafe to do it.
Instead of porting, we have hybrid codes. After all, you can link Fortran and C/C++, and if you make a C interface around your Fortran code, you can call it from Java. Modern codes here have C/C++ components that make calls into old Fortran routines, and if you do it this way you get the added benefit that Fortran compilers are screaming fast, so the old code continues to run as fast as it ever did.
I think the best way to handle this is to do any porting you need to do incrementally. Make a lightweight interface around your old fortran code and call the pieces you need, but only port things as you need them in the new part. There are also component frameworks for integrating multi-language applications that can make this easier, but you can check out Conversion of Fortran 77 code to C++ for more on that.