I have a disk layout like this:

That is XP on /dev/hda1, a gentoo boot partition on /dev/hda2, and a gentoo swap, gentoo root, and FAT32 partition inside an extended partition. Unfortunately, the extended partition has about 5 or 6 GB of unallocated space at the end. I would like to use this space for the 4th primary partition to install FreeBSD. Is it safe to use QTParted to shrink the extended partition and then use the allocated space to create a 4th primary partition? Or will this screw up Linux?

Note: /dev/hda2 is ext3 and /dev/hda6 is reiser

i do this kind of crap all the time. write down the starting and ending cylinders for each partition
/dev/hda5 399 465 506488+ 82 Linux swap
/dev/hda6 466 2791 17584528+ 83 Linux
/dev/hda7 2792 2857 498928+

delete your extended partition in linux, NOT windows, then recreate the extended partition for cylinders 399-2857. then recreate each of your partitions, keeping them the same type as before, and most importantly, the same starting and ending cylinders.
then you will have the same free space from 2867-the end of the disk to make another partition. if you type something wrong, exit without saving and start over. mine is similar to yours./dev/hda1 * 1 260 2088418+ 6 FAT16
/dev/hda2 261 1500 9960300 c W95 FAT32 (LBA)
/dev/hda3 1501 23000 172698750 85 Linux extended
/dev/hda4 23001 24321 10610932+ 83 Linux
/dev/hda5 1501 3500 16064968+ 83 Linux
/dev/hda6 3501 3700 1606468+ 83 Linux
/dev/hda7 3701 4000 2409718+ 83 Linux
/dev/hda8 4001 23000 152617468+ 83 Linux


parted is probably safe too, but i haven't used it for that. linux fdisk just edits the partition table and doesn't do much else. the windows fdisk will blank the first so many sectors of a partition, ruining it, and besides, will not let you create partitions by starting and ending cylinder.
if you you get a starting location cylinder wrong for a logical drive, the logical partition information will overwrite data at that cylinder. that's the important thing not to mess up.