If you look through previous posts, you'll see this topic has been covered many times.  You'll also find that everybody tends to have their own opinions.  

It may help to tell us why you are visiting San Diego.  Are you visiting for fun?  Or will you be operating your agency during your stay?  Where I would recommend a tourist to stay is different from where I would recommend a provider to stay.  

Because you posted on this board, I'm going to assume you would like to know where you could maximize your business.  My recommendation would be Misssion Valley.  There are tons of hotels, plenty of parking, and centrally located.

I hope this helps.

Both Mission Valley and Mission Bay are convenient to many gents. DT and Gaslamp can present problems traffic and parking wise IMO.

I am going with the consensus on this one.  Its all about location, location, location.

Mission Valley is centrally located, meaning you can draw from the North, South, East, and West (Beach Areas).  Great Parking, Restaurants, etc.  Also, its close to all of San Diego's attractions.

Have fun.