Moved library to new laptop, but it didn't take all playlists and apps

I got a new laptop recently and have been trying to phase out my old desktop. I followed the instructions for moving/importing your library. Things were made a bit simpler (I think) because my library was held on an external HD that I now have connected to teh laptop so there wasn't a lot of file moving involved. The trick now is that I open iTunes and it lists all of my playlists, but only the smart playlists still have all the associated songs. The "regular" playlists are all empty and the main window instructs me to add music by dragging it to the playlist, etc.. Also, when I connect my iPhone and attempt to sync, I can see that a large portion of the apps currently on my phone do not appear on iTunes. I get a message warning me that syncing will erase and overwrite what's currently on my phone so I've avoided syncing for several weeks now.
I still have my original desktop with iTunes installed and I only need to connect the original external drive to get back to where I was before the move. I haven't deleted anything so I could try it all again, but I would imagine the same results. Is there something I've missed? I tried asking at the apple store and was told the only solution was to create all of my playlists again "by hand" and then contact itunes to see if they would "allow" me to get credit for all the missing apps and then purchase them again from the store. There has to be another way.
Thanks for reading and any help you can offer

When you copied the music from your old computer you should have included the iTunes database (iTunes Library.itl) as well as your media files - this is the structure (normally in C:\Users\username\Music) that you should copy from old to new:
If you only copied the media, and not the database file, try doing so now (without iTunes running) - the files and folder structures should be the same on your new PC as on your old one.
Then hold down SHIFT while starting iTunes; you'll get this prompt:
Click on Choose Library..., then browse to and select the iTunes Library.itl file that you just copied. Your library should now be in the state that it was on your old machine, including your playlists.

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Moved library to new laptop, but it didn't take all playlists and apps

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