I'm not trying to make this more confusing, but it's not as simple as just fixing each disc separately, or fixing the entire show all at once. You should look at it from the perspective of musical sets. By musical sets I mean sets of music as played by the band, and you should look at fixing each set regardless of whether a particular set spreads over more than one disc.

So the first thing you look at is whether the show you have was played as a single set or as multiple sets by the band. You are almost certainly not going to want to fix an entire disc as a disc if there was a set break in the middle of that disc. Instead you will probably want to fix all the files of the first set as a set.

Also load up the last song of a disk and the first song of the next disc together in your computer's audio player and listen to the transition. Is it seamless? If the audio between two discs is actually seemless then that's a good reason to fix those files together because you want to preserve the seamless transition. If you were to fix your files on a per disc basis, you would end up introducing silent padding that will ruin the transition. You won't hear this if you burn the tracks to their respective discs, but the reason that this is undesirable is that you can never tell in the future how someone else might burn the tracks to a disc. CDs are getting longer all the time, and what was a good layout for the old 74 min discs may suck on 80 min discs, and be even more useless if 90 min discs catch on. Don't introduce a problem into your files that you or someone else will regret later when longer discs become the norm.

Confused? Well let's look at the show in question:

Disc 1 63:52.80
01 Intro 05:31.78
02 Bartender 08:10.92
03 When the World Ends 05:27.93
04 Busted Stuff 04:45.04
05 Two Step 09:18.04
06 Everyday 06:20.89
07 Grace Is Gone 06:48.74
08 Grey Street 04:22.85
09 Best of What's Around 06:09.04
10 Tripping Billies 06:56.80

Disc 2 66:25.45
01 The Stone 07:52.88
02 Gravedigger 05:14.02
03 Stay or Leave 05:34.52
04 Warehouse 09:44.97
05 Where Are You Going 05:05.50
06 Tim Solo 07:23.31
07 The Maker 06:21.22
08 Crush 10:02.57
09 Don't Drink the Water 09:06.46

Disc 3 69:21.95
01 Exodus > 03:22:01
02 Cry Freedom 06:39.50
03 Lie In Our Graves 10:52.22
04 Pay For What You Get 05:53.58
05 Tim Solo 07:11.31
06 Jimi Thing > 06:11.40
07 What Will Become Of Me 02:44.12
08 #41 06:43.05
09 Ants Marching 07:59.50
10 Nancies Intro 03:38.18
11 Dancing Nancies 08:07.08

I can't tell from this if there was a set break. Maybe there was a set break at the end of disk 1, maybe not. So load up Tripping Billies and The Stone in your audio player, skip forward to near the very end of Tripping Billies and listen to the transition. If it's seamless, then make a note of that. Do the same with Don't Drink The Water and Exodus. If the transition there is seamless you will want to fix those tracks together. I.e. if both transitions are seamless then fix the whole show together. If there is a fade out/fade in or some other obvious cut between each disc, then fix them per disc. If there is a cut at the end of disc 1, but discs 2 & 3 are seamless, fix disc one separately then fix discs 2 & 3 together. I hope this makes sense.

If you happen to know that there was a set break between, let's say, Gravedigger and Stay Or Leave, and the transition between discs 1 & 2 is seemless, then you would fix disc 1 AND the first two tracks of disc 2 all together.

Also, I do the same thing with encores. If the show has an encore I listen to the transition between the last song before the encore and the encore. If it is seamless then I fix the encore along with the tracks before it. But if it is not seamless, I fix it separately, which sometimes means just padding the end if it needs it and the encore is just one track.

One last thing I would say is it is better to err on the side of fixing the whole show at once than on fixing it it in parts, if you are unsure about what you are doing. If you fix it all at once the worst that can happen is that miniscule portions of one track will end up tacked on to the beginning or ending of an adjacent track. Although this is not technically perfect, it is essentially inaudible and is 'good enough' for most people (although maybe not for trading purposes). Whereas if you fix each disk separately but one or more discs were seamless, that seamlessness will be lost and if the tracks are ever burned to CD in a different layout than that proposed, a pop may well be audible between the tracks that were originally listed on separate discs. That's why you hear people say to fix the whole show at once. But being the anally retentive perfectionist that I am I never just run shntool over the entire show w/o considering set changes and encores.