Try using Cool Edit.It enables one to see signals both in time- and frequency- domain.
Audio-in suffers the following limitations:
-limited bandwidth.If you want to measure 5th order distortion of 20kHz signal,you need sample rate over 200kHz.
-no DC signals can pass through the input capacitors.
Accuracy is always a problem by measurements via soundcard, because there is no reference!
In TrueRTA you can make a calibration with an AC voltmeter for the voltage level, for the frequnecy response there is a selftest utility with a sweep test for calibtrating the soundcard signal path.
Today computers sound cards has really powerfull DSPs that has a goods samples bitrates with a great resolution and enough accuracy for major aplications even has from 2 to 7 out channels for analog control projects.
The really important is the interface design, you should be sure that whatever you connect in the input of you Sound Card won't put in risk your sound card and your PC.
Labview from National Instrument is a good idea but if you really want to develop your Acoustic Analizer from the begining i recommend use MATLAB (Data acquisition toolbox, DSP toolbox) and MATLAB Compiler for C++ programmers.