To start things off, I'd like to give a quick rundown of my usual working method with audio. For the most part I utilize sound samples and recordings as my means of composition (we'll call that music concrete style work), though I'm getting further and further into synthesis techniques everyday now. I also regularly write acoustic music using lilypond (no GUI, just hard coding straight into lilypond), but even then I'm inclined to sample/quote other music in my creation process. I personally think my inclination for twisting samples stems from my DJ roots.
To record things I generally either use Ardour or Rezound though there are tons of different recording apps loaded onto my computer (not to mention the audio programming lanugages that can all be used to record). If I just want the audio file as a sample Rezound is much faster and simpler to use, but if I know what I'm recording is going to end up in an Ardour session anyway (such as if I'm recording soundscapes etc...) then I'll record straight into Ardour.
Rezound's editing capabilities are quite nice. It gives remarkable feedback for clipped samples (a bright pink bar against the blue/green background); even if it's just one sample that's clipped, it will be visible at any zoom ratio. During recording, it's dialog gives a count of the number of clipped samples as well as a very responsive volume meter. It also comes with many essential wave editor functions such as mix paste, resample, curved gain, LADSPA plugin support, various looping playback modes, and a bunch of built-in effects, such as a convolution filter and morphing arbitrary FIR filter (essentially a parametric eq that can change over time). These don't quite give the same flexibility that Ardour's LADSPA features do, but for a wav editor I'm VERY happy with rezound. Furthermore it can function perfectly fine without jack running, which is nice if I ever run into troubles with jack (or freebob for that matter).
Ardour should need no introduction. It's the behemoth of the linux audio world - better than pro tools in my opinion. It's octophonic mixing capabilities are one of my current favorite features as SFU regularly allows me access to octophonic performace spaces. With it's ability to automate LADSPA plugin settings, not to mention it's ability to host them in nearly any combination imaginable, nearly any sound needed can be achieved. Generally I use Ardour as my music concrete composition tool, arranging and tweaking samples as I see fit. I then use it's export feature to bounce everything down to a wav output file or perform it live through my soundcard (a Presonus Firepod) depending on the situation.