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My current bootloader is two-stage and works by having the first stage scan the FAT filesystem for the second stage, load it and jump to it. However, I would like to be able to use non-FAT filesystems in my OS, and I would not like to have to have a FAT partition on whatever disk I boot from. How easy is it to implement a simple filesystem scan for a better filesystem (I'm thinking ext2/3) in a first-stage bootloader? What are my options other than putting the second-stage bootloader in the filesystem?

I'm guessing not that hard - GRUB does it for ext2/3 at least, along with a few other fses, all in one block. It seems that ext2 uses the normal inode ((double | single) indirect) block list for files, and since the stage2 will be relatively small, it probably would only use a direct block list, which would be easy to read. You could even hard-code the position of the stage2 in the filesystem tree into the stage1 when you install it, and then you wouldn't have to do a recursive search.

Edit: and a scan for the correct filesystem would be completely trivial - pretty much all filesystems have some sort of magic number in their first few blocks that identify them.

One way is to write a separate bootloader for every FS you wanna support...
And then have the Setup program choose one depending on the partition the user selects.