How do I move applications from an external HDD to rMBP?

Hi all,
My late 2009 unibody Macbook met an unfortunate demise due to some spilled water (I think the logic board is dead), so I upgraded to a late 2013 13" rMBP. I wanted to move the applications on my Macbook onto the rMBP, so I purchased a cheap HDD enclosure with a USB 2.0 connection. After removing the HDD from the 2009 Macbook, I connected it to the rMBP where it showed up as Macintosh Harddrive on my desktop, so I was able to move several important documents over to the rMBP. But I can't quite figure out how to move my applications (Office, Keynote, Adobe, etc.) on to the rMBP.
I tried using Migration Assistant, but it made me move the old user profile on to the rMBP (I didn't want to write over the one I started for the rMBP), which I eventually just deleted (the migration took 4 hours, I couldn't find my applications, and I didn't want to have to switch profiles to use the applications anyway). What's the least painful, hardest-to-screw up method of moving applications from the old HDD to the rMBP? I thought about downloading each individual program again (I don't have the physical media anymore) and entering in the keys (which I have for Office). I also think I might have purchased and downloaded some applications through iTunes? Maybe I can re-download through there?
Any suggestions are greatly appreciated.

Migration assistant would actually be your best bet. While setting up Migration Assistant, it should ask you what you want to move, with tick boxes for Users, Applications, Settings, and "Other Files and Folders." Untick everything other than Applications, then they should install to your /applications folder. Photo #8 here (under the "Time machine or other disk" section) shows what I'm talking about.
Just dragging and dropping applications may work for SOME applications as they are packages, most need supporting files, preference files, etc...

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