at least you don't run into the problem that within your application you seem to have two files which are conceptionally different (such as Makefile and makefile), but end up being the same file on the OS level.

at least you don't run into the problem that within your application you seem to have two file names which are lexically identical (such as Makefile and makefile), but end up being the two different files on the OS level.

It cuts both ways. If you really see this as a problem, you should cut out uppercase from unix usage too.

I don't think case should be enforced programmatically in either environment. There are too many situations where mixed case might be seen as a benefit.

I try to stick to lower case letters unless the circumstances really beg for upper/mixed case.

In general, I tend to base it on who is the intended consumer. If it's a person, spaces and capitalisation are used. If it's a program, underscores and lowercase.