Is there anything to consider if I want to share a Time Machine backup drive between a Lion machine and a Snow Leopard machine (a USB drive that I would be rotating between the two computers)? Obviously I cannot use encryption (since Snow Leopard will not be able to use the disk), but are there any other gotchas? For example, will Spotlight behave (i.e. not constantly re-index because of the version change)?
In general, there are no issues or side-effects of using a drive connected in turn to any number of macs with mixes of OS levels since each Mac only writes to its own backup folder.
The obvious exception is Lion style FileVault encryption where Snow Leopard and older macs will be prevented from reading or writing the drive.
The only other problem is if you mix lion and snow leopard on the same Mac and (or) let lion "inherit" the backup of another machine.
In that one case, the contents of the backup are mixed and you can't be guaranteed a restore of system files will work. Your data and pictures and other files will be fine but anything tied to database files or a specific version of the mail app (for example) can depend on versioning.
This isn't really a side effect of Time Machnie changing how it works, but of the OS and app changes.
My initial experience so far is that a Snow Leopard backup not visible from Lion (even if it was the same machine being upgraded). If you enter Time Machine after the upgrade in Lion your earliest backup that you could recover to is at the point Lion is installed - I had to browse and compare the sparsebundle to pull out all my pre Lion files.
Having said that, I would recommend creating a separate sparsebundle for your Snow Leopard install (or your secondary OS). It is not difficult to do and it keeps a separation of the two operating systems. Please reply back if you wish to investigate down this path.