Blessed Silver, Static Transferral, Hungry Stalactite: effect is minimal that you barely notice the different (all of them give~5% damage output)
Acute Tracking: since it got some attention in previous patch, assume it's working. If you have a high dodge chance or can stay invisible most of the time then you should use it. From my experience it does seem to increase your damage though can't say for sure how much.
Sparking Dart: doesn't offer much as it should be, roughly 40% instead of 200%
Life's first movement: you should only use this if your rage conversion time is high (8 - 10s) and your spell/attack has low cooldown / resource cost. Otherwise you'll find yourself 0/10 or 10/0 most of the time. Don't use with channeling spell (Thunderstrike, Infinity Blade,...) because each instance of damage count as one spell cast. Whether it actually increase damage or not, I can't tell. No different in stats on character sheet.
Branded Burst: 100% working. Your best friend if you don't invest point in toughness. Work best if you have high dodge chance to avoid lose stack from swarm of trash mobs. Avoid damage over time effect (ailment and ground effect) since each tick reduce one stack.
Tethered Shade, Waltzing Smoke: working. but Waltzing Smoke doesn't increase damage after breaking invisibility. Atleast it doesn't show in character tab. These are great combo if use along with Branded burst. Also distract some hard encounter like the Justicar of the Republic so you can flank him from other side without dealing with that shield.
Safe from afar: doesn't work.
Archion's teaching: work for some projectile attacks but not for some others. Doesn't work for gunslinger and railgun. Maybe more.
Meditative focus, Persistence hunting: seem to work in the beta but not sure atm. If you don't have anywhere else to put point to, pick those since they're suppose to give you 25% multiplier. Tell us know if you find out they're working or not
All of this were tested in mandate mission using a spawn crystal (the one that spawns mobs when you get near), Haulstone or whatever they call it. Pick everything in the skill tree except the aforementioned nodes then shooting them multiple times to find out the min-max number of one attack before picking the nodes to see if there's a different. Also in 1.0.4.0 patch. None of them are affected by recent patches anyway