Indeed, and I've yet to get a handle on this. Is there a guide written specifically for Shadow tanks that advises on when to use Resilience on certain bosses' attacks?
No. There are TORParse combat logs, however, which form a decent starting point.
For HC (HM+), here are my thoughts:
Z&T - Overall low DTPS, so not essential to micromanage. Maximize Shroud/Resilience uptime on Zorn, and cycle between on-use relic and Deflection on Toth (covering gaps with Absorb adrenal).
Tanks - If tanking Stormcaller, Shroud shortly after engaging and after each defensive systems when you resume normal tanking. There's a predictable Electric Discharge shortly after each engage point, which is the largest spike of damage, and you'll also negate at least 1 regular attack.
Stormcaller's damage is insanely predictable. He uses Zap Attack every 3s or 2s after Electric Discharge. He uses Electric Discharge about every 11 seconds, but that is frequently interrupted by DD or defensive systems. He uses Double Destruction 15 seconds after each tanking phase starts (and obviously no attacks while DD is channeling). He doesn't actually resume attacking you for 10s after beginning to channel DD, so you have a while to sit and spin at that point.
During floor tanking phase, you take a hit from Mortar Volley every 3s. "Lightning rods" land every 6s (coincide with every other Mortar Volley hit) I believe, but it's been a couple weeks since I've done EC and I never explicitly timed it.
I've never actually tanked Firebrand (never saw a reason to, and taunt swapping is easier than tank swapping), so I don't have specific data to help there. However, as he's pure M/R, Resilience/Shroud is obviously not of any great use.
Vorgath - Use to negate damage from Sticky Grenade. Everything else is M/R. If anything is hitting in the minefield, there are deeper problems.
Kephess - The most obvious one is on Kephess himself, when he leaps into the air. You can see his shadow on the ground before he lands (assuming you have shadows on) to predict the exact moment of landing. Hitting Shroud as he lands will negate the damage from Empowered Slash and the first couple ticks of Savage Wounding (assuming, of course, you've taunted him). In a pinch, it can also be used if you misplace a purple circle and need to cross through one whilst still affected by Breath of the Masters.
Another useful time to use Resilience/Shroud is immediately upon engaging Baradium Bombers. If you start with a Shroud+Taunt, you can nearly always force the first Rocket Blast onto yourself and negate it. After that point, the BB is probably chain-stunned until dead, but avoiding the first Rocket Blast can be tricky.
Yet another is for the Trandoshans, you can Resilience/Shroud > Slow Time/Wither for extra threat on the Trenchgutters when they pop if you're called upon to tank them. EC NiM strategy is generally very different from HM and this may not be relevant depending on how you handle it.
You could also use it to blank Channeled Pulse from the Pulsar Droids, especially if you're intentionally lagging behind during the first or second changeovers to increase the odds of drawing any Rail Shots during the swap.
I'm out of time for the moment, so I'll append this at some point (or someone else can) with TFB HM data and/or EC NiM changes. I'm leaving out EC and KP for the time being because they're probably not a major concern of progression raiders, and even the high DTPS of KP NiM is not a detriment to clearing it easily.