I have a MacBook Pro running Snow Leopard and Ubuntu on separate partitions. I use rEfit to choose which operating system I want to boot into. I would like to upgrade to Lion, but I'm concerned this will cause major problems due to my partitioning scheme. Has anyone else done this?
I used to dual boot fedora and snow leopard on a macbook pro and upgraded it to Lion no problems. You should just be able to upgrade as normal without altering your ubuntu partition, although as per Vlads answer it's always best to take a full backup first (not that I'm always very good at following that advice myself).
Lion upgrade should not touch your Ubuntu partition (unless you choose to repartition/format the disk). You might need to reinstall/update rEfit as well to be able to boot into Ubuntu after upgrade.
I highly recommend you take a full backup of your disk image before the upgrade to an external drive. Better safe than sorry!