I read this Tidbits article a short while ago and realized this has been what’s been driving my somewhat nuts on my Macbook Air, with Lion. I have a lot of apps open, typically leaving everything running for days at a time, through sleep and wake. I would frequently cmd-tab and find that the apps weren’t listed. This tended to be infrequently used apps, or at least ones not used for awhile. A weather app, Preview, BBEdit and even browser windows. When I restart the app it loads in its previous state so that hasn’t been a problem, but it’s counter-productive to try and task switch, fail, and then have to start the app again (I tend to type the name in Spotlight).
This is one area of Lion that hasn’t improved my user experience and isn’t something I would expect to learn to like. Providing an inconsistent app switch is not an improvement.