I worked for both, a small (25 people) and large (6000) company.
Both experiences are very very very different. For me personally, a smaller company gives you more meat for your essays. Its hard to demonstrate impact and leadership within a large company. At the big company, they are so stringent with so many rules and regulations to the extent that when I am cc'd on emails going out to clients, the people in the cc list are listed in order of rank. its retarded sometimes.
The smaller company was a lot of fun. A lot more casual to say the least. I was also given more and bigger responsibilities and promoted in just over a year to a team lead role. The same role would take an average employee at the big company about 4-7 years to achieve.
From a business school application point of view, a smaller company gives you more material to discuss. It also provides you with more intimate recommenders.
As for the big company, I highly doubt the AdComm would have ever heard of my company, even though we are the world leaders at what we do, with global presence, and about $4 billion in annual revenue (my department of 160 generates $80 million). I feel the AdComm may know the general Fortune 100 companies, but not the niche companies, even if they are quite large.
I am also requesting my previous boss from my previous small company job to be one of my recommenders.
I still haven't figured out if I made the right move in moving to the big company. I guess only time will tell.