There is no clear 'road map' for every program ever made on how to move it from one computer to another, period. As LH as said, besides the primary program folder, almost ALL programs put other parts elsewhere. Parts can be under the folder USER, in the Registry, in the various C: drive folders such as Windows, Program Files, Program Files (x86), Program Data, and sub-folders under those, as well as other named folders.
The Windows Easy Transfer generally will allow you to 'move' and then 'merge' back MS programs and Windows customization you have done. PC Mover by LapLink will do more in that not only what Windows Easy Transfer does, but other non-MS programs as well, but by no means all.
Doing an in-place Install, an Upgrade, generally speaking will keep almost everything that was on the system before. The reason being is that they keep the old file structure AND contents that was there when the Upgrade was started. That means ALL the 'parts' needed to run all your programs remains. It means that the entire Registry is retained, and instead of creating a new one, it either ADDS or REPLACES entries needed to RUN Win7. The process first copies non-Windows specific files it finds into 2 saved folders in case you should need something it missed. Then it starts replacing files upgrading them to the needed levels. No guarantee it will work 100% and there is a chance you'll either need to re-install some programs or locate data that wasn't moved, but generally speaking, it (upgrade) does a good job.
I also should tell you, depending on your h/w, and how many programs you have, it can take a significant amount of time. Mine took 3 1/2 hours to complete the upgrade, and I have an Intel i7 -920 with 8GB's of RAM. There were times I thought NOTHING was happening, all I saw was the drive light flicker, and I had to resist the urge to turn the computer off and try again.
As for 'merging' the Registry, no, you can't. The best your could do is save parts of the old one and load those parts into W7's once installed. However, it isn't easy determining what you need always. Many programs hide the license in the registry, but it is encoded that you can't recognize it, and may not even be in a hive you would associate with a program.
A 'back-up' program that saves the entire disk image will not work either. Well, if you can 'open' the back-up and retrieve individual files, it would, with a lot of work (see first paragraph), such as Norton Ghost which has an image view/explorer, and allows single file recovery.
For most users, an Upgrade is the best way to accomplish what you want. Next best choice is a transfer program, and the completeness of the amount of programs transferred is dependent on the transfer program used.