Let me give you some PROPER ADVICE...
I know exactly what you're asking and I'll tell you now that it's possible to do what you want and it's relatively quite easy. Most people don't know or are unaware... but I do it all the time because I reinstall Windows 7 about every 6 months to keep it running smoothly.
BEFORE YOU DO ANYTHING... you need to backup some important data.. I'll tell you which data. In fact, what I'll do is tell you what I do on my computer... it might make it easier for you to understand, ok?
I have one SSD (Drive C) and two mechanical HHD's (Drive D & Drive E). I keep the O/S, browser, media players... on Drive C. All of my games and misc. programs.. I install onto Drive D. I use the last HDD, Drive E, to keep all my backups and media files (photos, music, videos, and download folder).
If I want to perform a reinstall of Windows onto Drive C... I go to Folder Options and uncheck the option to hide hidden folders so I can access the data some programs and games store in AppData & ProgramData.
First, I create backups folders like Appdata-local, Appdata-roaming, and C-Programdata. Note you could use the same names but sometimes Windows will think they're hidden folders and will hide them.. so I alter the name slightly but close enough for me to know where they belong.
Next, I go to the C\Appdata\local folder and look through the list of folders with data I want to copy and bring over into the next install. I only do the ones I need, like any game saves or profiles. You have to look for the game name or publisher or developer. I then do the same thing inside the ROAMING folder. I also like to copy the Mozilla folder so I can copy my Firefox profile completely.. and I also do like Skype so I won't lose my past conversations. Then I perform the same task inside the ProgramData folder... just make a copy so you won't lose the data...
I then perform my reinstall of Windows and copy that data back into those same locations so the data will still be there.
As for the shortcuts... all you have to do is go to the install folder for each of the programs or games you installed onto the other drive and create a desktop shortcut for each one... I usually just edit the shortcuts when I'm done to get rid of the "shortcut" suffix at the end and drag them into my start menu or Games Explorer folder... and then you're done.
I've found that this trick works about 95% of the time... and you don't have to reinstall the program or game all over again..
If this will be your first time.. I would recommend that you just copy over the entire AppData and ProgramData folders at first until you become familiar with which programs you need/want to copy in the future. That way you'll have everything and won't have to worry about accidentally skipping or missing something. Just don't copy over anything that was created by Windows.. Only do like your games or certain programs like your browser.
If you have any questions.. just hit me up.