Apple would probably tell you to use Journaled HFS+ with case-sensitivity turned off. This is really the best bet from the standpoint of compatibility with Mac applications and utilities.
You mention NTFS, which, by default is read-only on a Mac. NTFS is perhaps the best Windows filesystem out there, but it's overall a mediocre one (no journaling, fragments, etc.) and its features are divergent of UNIX/POSIX ones filesystems (no symbolic links until Vista, standard file mode flags, uids and gids, etc.). However, if you're comfortable with getting you hands dirty in Terminal.app, you can download the [Mac port of Linux' FUSE|http://code.google.com/p/macfuse> (a kernel extension that permits loading of user-space filesystem drivers) and the [NTFS-3G|http://www.ntfs-3g.org> driver for it, which provide a fully read-write NTFS filesystem for your Mac (never tried the Mac version, personally, but the Linux version works famously).
You can similarly obtain a kernel extension that permits the Mac to [read and write Linux EXT2 and EXT3 (as EXT2) filesystems|http://sourceforge.net/projects/ext2fsx]. Generally speaking EXT3 is a more reliable and better performing than Mac's HFS+, but it's always case-sensitive, and the Mac implementation might have some issues. The Mac driver, however, doesn't support journaling. You can download [EXT2/3 support for Windows|http://www.fs-driver.org> too.
Ideally, everyone would use [ZFS|http://en.wikipedia.org/wiki/Zfs] -- but it's not likely that Windows will have any ZFS support any time soon. It's basically only available for UNIX and UNIX-like operating systems (e.g., basically everything except for Windows).