Question: My application has potentially a huge number of arguments passed in and I want to avoid the memory of hit duplicating the arguments into a filtered list. I would like to filter them in place but I am pretty sure that messing with argv array itself, or any of the data it points to, is probably not advisable. Any suggestions?

Answer: 
Empirically, functions such as GNU getopt() permute the argument list without causing problems. As @Tim says, as long as you play sensibly, you can manipulate the array of pointers, and even individual strings. Just don't overrun any of the implicit array boundaries.
The only time I would say that directly manipulating argv is a *bad* idea would be when an application changes its behavior depending on the contents of argv[0].

However, changing a program's behavior depending on argv[0] is in itself a very *bad* idea where portability is a concern.

Other than that, you can treat it just like you would any other array. As Jonathan said, GNU getopt() permutes the argument list non-destructively, I've seen other getopt() implementations that go as far as serializing and even hashing the arguments (useful when a program comes close to ARG\_MAX).

Just be careful with your pointer arithmetic.