hmz, this reply is getting long...
all opinions derived from years of fiddling.
AFAIK Windows completely ignores the MBR of "removable media" and blindly jumps to where the first partition should start, that means it shouldn't be able to see any partitions that start somewhere else.
As the SD card appears just like any other block device, you can use a MBR with it and therefore have multiple partitions on it, you just won't be able to use the other partitions in Windows.
Are you *shure* about that, that sounds awful lot like windows 98? i have several usb devices with multiple partitions, they all show up just fine in windows (NT 5 or 6). In NT5 or older they do have to be properly ordered in the partition table. having 1 partition defined on row 2-4 with row 1 zeroed out is asking for device manager trouble. had problems wit this in win2k and XP SP1 (you have 3 partitions, you delete 1 & 2 then grow partition 3 => 1 partition defined on row 3)
anyhow, my opinion on FSes:
FAT
pro: when the light stops blinking, your data is on the device, yank it out and plug in another machine
con: no large files
NTFS
pro: large files, best choice for windows users.
con: needs to be safely removed or old kernels (pandora kernel) will refuse to mount it and then you need a windows box to properly remove the drive. This *issue* seems fixed in modern kernels. theoretically you only need to safely remove after writes in windows.
EXT2
pro: every linux box, even your coffee machine and dishwasher can read this (provided they run linux ;-) ), there is a driver for windows
con: if you do not safely remove you are fsck'ed, usually you can recover from this but the recovery process takes ages
EXT3
pro: better protection from power failure (like yanking out the device) much faster recovery, compatible with windows ext2 driver
con:
EXT4
pro: faster then ext3 depending on the kernel/program you measure
con: different default settings among the latest kernels, not stable in older kernels and the windows driver does not work
short summary: use NTFS or EXT3
both are *default* for an entire platform and work on other platforms with an additional driver. just count the number of driver installs you would need to perform and choose the least amount of work
EXT4 disclaimer:
I realize i just went hard on this FS but we are talking about removable media, not root partitions