The following is a recipe for a comparison based on filenames alone, not based on file modification times or even content checksums. But it's a start :) Also, the below is to compare two directories that are both on Google Drive, but you can easily adapt it by generating a list of your local files instead with some call to ls. (So obviously, the below is a recipe for Linux.)
1. Install and configure drive
drive is a Linux command line client for Google Drive. The easiest is to install it from a package.
After that:
Change into the directory on your computer that includes your whole files synced from Google Drive:
cd /home/user/example-dir/
Initialize drive with access to your Google Drive. This will ask you to visit a URL and paste the auth code you get there, and save this in a config file in the current directory.
drive init
2. Comparing directories
I found that for large Google Drive folders (36 GiB of small files in my case), starting by comparing directories and fixing cases of missing directories was a good first step. (Also because drive has no option to copy directories without the files inside between two Google Drive folders. Not a problem if you compare between local and remote files only.)
drive list -directories -recursive -no-prompt -sort name "source dir" > DirDiff.1-source.txt
drive list -directories -recursive -no-prompt -
sort name "dest dir" > DirDiff.2-dest.txt
vim -es +"%s/^\/source dir\///g" +"wq" DirDiff.1-source.txt
vim -es +"%s/^\/dest dir\///g" +"wq" DirDiff.2-dest.txt
The drive command obtain lists of directories from Google Drive, and the vim commands remove the differing base directories from each path so that comparison will work properly.
Now to list the directories that are only in the source tree:
comm -23 <(sort < DirDiff.1-source.txt) <(sort < DirDiff.2-dest.txt) > DirDiff.3-missing.txt
And to show the directories that are only in the destination tree:
comm -13 <(sort < DirDiff.1-source.txt) <(sort < DirDiff.2-dest.txt) > DirDiff.4-added.txt
About using comm like this, see here.
3. Comparing files
This works very similar to comparing directory trees:
drive list -recursive -no-prompt -sort name "source dir" > 1-source-files.txt
drive list -recursive -no-prompt -sort name "dest dir" > 2-dest-files.txt
vim -es +"%s/^\/source dir\///g" +"wq" DirDiff.1-source.txt
vim -es +"%s/^\/dest dir\///g" +"wq" DirDiff.2-dest.txt
To show the files only in the source tree:
comm -23 <(sort < FileDiff.1-source.txt) <(sort < FileDiff.2-dest.txt) > FileDiff.3-missing.txt
To show the files only in the destination tree:
comm -13 <(sort < FileDiff.1-source.txt) <(sort < FileDiff.2-dest.txt) > FileDiff.4-added.txt
The solution you describe is the best solution.
I personally have "email@address.com" as my top level in my different Google Apps accounts, and I bookmark that page (where I have browsed into that folder) in my toolbar.
This seems to be the best solution for me, and at a glance it is very obvious which folder I want in my other drives.
On a day to day basis, just clicking on that bookmark is enough to get me into the folder that I treat as "root"
You can also use a URL shortener to create links like blah.blah/persdrive that you can then use on public/shared computers where you don't have your bookmarks. I do that for my Google Apps for domains to avoid typing the whole google.com/a/domain.com every time
Best Answer
The easiest way would be to make a top level folder called "Business" in your business account, and a "Personal" folder at the top level in your personal account
Then place ALL your business folders below "Business" in your business account and similar in your personal account.
Google Drive doesn't really see each folder as separate in that way. Even if a friend of yours shares an "Account" folder with you, and you already have 2 "Account" folders, it won't nest that any differently.
I personally have "email@address.com" as my top level in my different Google Apps accounts, and I bookmark that page (where I have browsed into that folder) in my toolbar. This seems to be the best solution for me, and at a glance it is very obvious which folder I want.