1, 2, 3, 4, 5...

Seriously, how do you want to count them?

We want to count the number  of documents  which has more than a size
of 50MB in the entire site structure. i.e. http://WSSTopSite. which
has more than 25 subsites  nested and having lot of document libraries.

I wanted to execute a query  or am planning to write object model
program to do that work..

What do you think is best?

Iterate thru all the lists in the farm.
If the SPList can be cast as a document library, iterate thru the list items.
If the SPFile associated with the list item is > 50 MB, count it.

But iteration method will not help to find  out complete count
in the site. because we dont know how many sites, how many folders
etc. we need to create a recursive method to find out a files and
folders. I feel this is bit lengthy and time consumming process.
anyway if anybody has some tectics to recursive the below requirement
let us know the same.

1. Open document library (dynamically).
2. Find out the number  of files in that document library.
3. If document library contains folders, enter inside the folder and
find out the number of files available in that folder.
4.Find out if there are any more folders.
5.If folders exist, repeat step 3.
6.Find out if there is anymore document library, if exist, repeat the
steps 1 to step 5.
7.This completes for one team site.
8.Iterate the same for all site.

Um iteration will definentaly work. Just 'foreach' through each VS.