When recording using a laptop rather than a stand-alone recorder, the software used will normally be AudioMulch. An alternative that is sometimes preferable is Plogue Bidule. Old-fashioned looking meters (to the BBC design I was trained to use) are courtesy of zplane's PPMulator.
The microphones we use all require their output to go through software processing before use. First the signals from the four capsules are converted to Ambisonic B-format, with the simultaneous correction of any unevenness in frequency response. Each of the microphones comes with its own software for this purpose, but there is a single program (or rather, plugin for audio editing programs) called VVEncode, from VVAudio, which is able to use the calibration data for any of the microphones, and so this is what I use. The SoundField SPS200 comes without individual calibration, so I had mine calibrated by Core Sound using the same system as they use for their TetraMic.
Depending on the requirements of the job, the B-format files may be edited as they are, or converted to stereo or surround first. Most commonly I edit the B-format, and generate the formats for delivery at the end of the process. Editing is usually a simple matter of tidying up the start and end of works or movements to form tracks for listening; but I have experience of editing together multiple performances or takes, as is common in studio recording. The bulk of my editing is done using WaveLab, from Steinberg. This can handle any of the formats I use at present, and includes the capability of burning CDs or DVDs, as well as formating output for CD pressing plants. I use plugins to decode the B-format into that which is required; either VVDecode (for stereo) or Wigware (for surround).
Sometimes a repair is desirable - for instance to mute outside noises like a passing siren, or more local ones like miscellaneous banks and coughs. not all such intrusions can be removed, but most can be reduced, and this may be necessary to make a recording listenable. WaveLab has a repair suite built in; but we also have available iZotope RX Advanced and Magix SpectraLayers Pro. In addition, Adobe's Audition, which in the past we used for editing, has a well-regarded set of repair functions.
The samples in the chamber organ are played using the specialised organ sample software Hauptwerk, from Milan Digital Audio; we have a public performance licence for the software. The samples themselves are taken from the Smečno organ recorded by Sonus Paradisi.