This is a complicated question to answer but I'll try my best to give you an idea.
When you say number of runways there are a few situations; this will vary based largely on wind as well as when and where the airport was built, but there are two main cases to consider. Keep in mind the wind may prevent the use of certain runways.
1: Side by side runways. Large airports like KPHL, KJFK, KORD (and even places similar in size to Van Nuys Airport) have parallel runways. This can greatly aid in throughput as two planes can land/takeoff simultaneously
2: Intersecting Runways. In this case you still have two runways but they will cross each other and depending on aircraft size cannot be used simultaneously. If the airport supports GA or the runways intersect towards their respective ends a land and hold short may be possible. With intersecting runways you would, in theory, have less options since you can't have the simultaneous situation you do with parallel runways.
Aircraft Size: another thing to consider is runway length and aircraft size. Generally speaking runways at a given airport are often of different sizes. As such some aircraft may require a specific runway, if, on a given day you happen to only be landing large aircraft you may only be able to make use of one of your two parallel runways even though both are useable in the current wind.
Taxi Ways: for what it's worth I would not think taxi ways are a limiting factor in airport design. They often are the place where the queue builds up but generally are not the cause of the queue.
Ground Crew/Ground Resources: If we are talking strictly commercial operations it takes time and resources to turn a plane around (get it back in the air). The plane may need fuel or a de-ice (de-ice facilities have gotten better and are usually near the runway now). You may need a tug, a crew to load the plane, food, cleaning … you get the idea.
Physical Obstacles: Some airports are built in areas with tough terrain. This may cause all departures and takeoffs to come in from a single direction. This can limit the amount of traffic in and out of an area as well.
Noise Abatement: With the growing concern for local communities and increasing noise of jet engines, some airports have growing restrictions on when you can and can't take off. I fly out of KPNE and they have restricted runway use on Sundays as well as no touch and go's at various times. In this case two airports with the same number of runways may have different throughput due to runway restrictions.
Runway Approach Systems: Not all airports have instrument approaches on all runways (or any runway for that matter, although with the addition of GPS approaches, more and more airports have some kind of approach). If the weather is bad the better equipped airport will always have a greater throughput (an ill-equipped airport may prevent landings all together, although that's unlikely for commercial airports these days).
The locale is a big factor as well; if you build a huge airport in an area that no one wants to go to or leave, it's not going to see much traffic. Likewise if you build a tiny airport in Central Park, chances are you will have a stream of planes heading to and from the Hamptons in the summer….