I may wait for more answers before I go experimenting with it, but if there are mining pools that let you merge-mine the scrypt based coins I'm wondering if I could set up p2pool to do it. I'm mainly interested in mining Litecoin and Feathercoin together without having to keep 2 instances of my miner running on every box. I'd think the version of p2pool at github.com/chrda/p2pool-fc should work. It says to only use it with Feathercoin, but I've checked the diffs against the official version and I don't know much Python (mostly Ruby on Rails) but it doesn't look like it should break anything if I used it for Litecoin.
I know it's pretty easy to set up p2pool to merge-mine Bitcoin and the other sha256 blockchains, just haven't seen any info on whether or not it's possible with the scrypt blockchains.
I'm still waiting for the Litecoin blockchain to finish downloading, hopefully by the time it finishes someone with more mining experience (or someone who knows the code better than I do) will see this and let me know whether or not it's a good idea.. otherwise I'll probably fall on my face a couple dozen times trying to hack together a solution.