If I understand your question, I believe that it is possible to do that. On a Mac, at least, I'm syncing a first gen iPod touch, an iPhone 4, and a first gen iPad, all with a varying set of apps and different sets of music and photos. I haven't had any problem at all.
But I think you might be asking if version 1.03 (the latest possible iPod touch version) of the app Shoot2Kill, for example, can coexist on your PC with version 5.5 of Shoot2Kill, the one that's iOS5 compatible. Not sure about that one - honestly never crossed my mind. If you'll give me a couple of hours I'll try to check and see if varying versions of the same app can coexist in the same iTunes.
It turns out that I took all the apps off my touch, but I have an iPhone 3 that hasn't been updated in at least six months. There's got to be something on there that's incompatible with the current iOS architecture, but it's syncing as I type this with no problems.
You've got your iTunes copied to your laptop - why not use the original copy for a little snooping? I think you'll find that everything works just fine.
BTW, there are several apps in the iTunes library on my desktop that are duplicated. I never could figure out why, but my guess is that some of them are versions that will run on one handheld and not the other.
Hope that helps.