Leaving CiM out of the equation, I'll probably go with Live at Budokan, especially because every other aspect of it is so good, makes James' weaker performance stand out more. They played another show not long before Budokan, plus the evening with format really wore him out (even though he got quite some time to rest, with the BTL jam and Instrumedley). James is huge favorite of mine, but this performance is a chore to listen to sometimes and hinders and otherwise nearly perfect release (I'm not 100% happy with the setlist either). He gets progressively worse, so ITNoG is a logical choice, but Only a Matter of Time is probably the low point of his singing.
I don't really like his Live in Tokyo performance either, albeit it's widely appreciated on DTF, he forced himself to much and doesn't always come out on top with that way over-the-top performance.
Live Scenes features some rough singing as well, but Portnoy is the worst offender there, he flat-out ruined the beginning of Home with those annoying accents (hiiigh-YAAAAAOOOOAAHHH). He acknowledges it in the commentary that he really hated how it came out and his vocals were never intended to be as loud in the mix as they ended up being. (We had an argument before on DTF about how much control do musicians have over the final product - this is an instance which proves that they don't always exert control over every aspect of the production). I like James' energy and timbre on this release (even the way he worked around not being able to reach the F# on LtL), although it's obvious that this wasn't a good live period for him (either).
He's hands off the best on Score and on the last two releases. His timbre, his range and power are all there and he often sings better (more to my liking) than in the studio version of certain songs, which never happened before. A good example is the last chorus of OTBOA on LALP and the "Hidden by disguise" section of ToT on BTFW.