800rpm unless you are using a fan controller. Reason why is because the fans are so close to the mesh on the top of the tj09 they will generate turbulence. I have found anything around 700-800 rpm mark is usually very quiet. That is why I always use 800rpm fans where noise is most prevalant - fan behind front of case, sidepanel fan, blowhole fan on top. And 1200rpm fans for rear of case as you generally won't hear that.
So for the TJ09 I would have 2x800 rpm fans (either Noctua's or Scythes) for the top, a 1200rpm fan in the rear, and possibly 1200rpm fans for gpu cooling and hard drive cooling as these fans in the TJ09 are not really obstructed so I don't think there would be much air turbulence (the hdd fan is sitting in a bracket between both HD bays, and the GPU fan is not flush up against the front of the case).
The 2 fans which comes with the latest TJ09 are already 1200rpm Evercool jobs so may be silent enough for the GPU cooling and as a rear exhaust, so you would only have to buy 3 additional fans. If not silent enough and you don't want to remove the gpu fan (tricky) and/or have to buy 5 fans in total, you could just buy a molex extension cable and volt mod it to 7v to quieten the fan down. Not sure if it clicks though.
The Silent Eagles are good but at 1000rpm I would not use them for gpu cooling or as a rear fan on the TJ09. They don't push enough air. And for cooling on the top of the case I think they would generate turbulence.
Of course if you bought a fan controller it would not matter - you could have any fan you want in there. But I generally prefer to run fans at 12v as I find at lower voltage their noise can be unpredictable. Most make a buzzing or clicking noise.
So for me the fan with the most airflow and best noise signature is the Noctua 1200rpm fan, usuable everywhere except in situations where the fan is obstructed by a grille. In that situation the 800rpm variety is best. The Noctuas also push about 20% more cfm's then the Scythes or Nexus fans at the same rpm level. (from findings at SPCR testing)