What is the problem about Praat? It is scriptable, so if you know what you want to do, you can do it. Of course MDVP offers some nice routines. In case you want to work on the signal itself also Matlab might be an option (toolboxes for signal analysis of especially: http://www.ee.ic.ac.uk/hp/staff/dmb/voicebox/voicebox.html)
Also audacity could be very useful in some situations. Although this software can be quite limited for a professional use, some functionalities of Audacity are flexible and easy to use. For example in audacity you can manage very easy multi-channel data and speech data with transcriptions, you can easily compute FFT and spectrograms, autocorrelation, pitch and other functionalities. Also, some functions to filter the signals with FIR filter are available. Many plug-in to extend the basic features are also present online.
For a more professional use don’t forget Matlab and the related toolboxes.