Faster Healing, Healer: Healing rate is never an issue.
Fixit, Speaker: There are enough skill points in the game without the need to waste perks on getting more skill points.
Earlier Sequence: Minimal impact on combat.
Cult of Personality, Presence: The reaction system is broken, rendering these useless.
Animal Friend: Animals are not a threat.
Strong Back: Inventory capacity is hardly an issue, especially with a party member to use as a mule.
Smooth Talker: Diplomat characters will have a good starting intelligence.
Silent Death only affects the first attack made, while Silent Running is a convenience.
Silent Death and Silent Running: Sneaking is poorly implemented and the perks follow the pattern.
Save scumming is effectively mandatory for any sort of normal gameplay, rendering the perk null.
Pickpocket: Failing at stealing causes everyone to turn permanently hostile regardless.
Lifegiver: The impact is negligible due to the level cap and limited number of experience points available.
Bonus HtH Damage and Bonus Ranged Damage: The bonus to max damage is too low to make a noticeable effect (short of using burst weapons).
Tag!: Can be used on Energy Weapons late in the game.
Quick Pockets: Improved access to inventory, but not as useful as the variant in Fallout 2.
Dodger and Toughness: Protection is good.
Slayer and Sniper: Ultimate combat perks that are usually not available in normal gameplay, due to the extremely high level requirement.
More Criticals and Better Criticals: Good pairing in Fallout, as the top perks are only available in the end game, if at all.
Bonus Rate of Fire/ Bonus HtH Attacks: Self-explanatory.
Awareness: Essential for any sort of planning in combat.
A quick breakdown of the usability of perks is as follows: Not all perks are equal due to the way the game is structured. For perks with multiple ranks the benefit listed should be interpreted as "per rank."