Not sure what you meant to ask ... but I'll try to answer the best I can.
I've heard both. And the rest of Jay-z's catalog, and most of the rest of the stuff released on the label.
"what we do" is my favorite song released on that label.
If you want to argue that other songs or albums had a bigger impact (especially songs off "Reasonable Doubt"), I won't debate that.
"what we do" is the song I would listen to most out of anything on the catalog. So, in my opinion, it's the best song from the label.
In short ... yes. Really.