Of course I think it's worth it.
I actually had extra AP to spend, so I put those into Bluff and Wand and Scroll Mastery.
Rogue Damage Boost I-II
Rogue Haste Boost I-IV
Rogue Deadly Shadow
Halfling Cunning I-IV
Halfling Guile I-IV
Subtle Backstabbing I-III
Toughness I-II
Assassin I-III
Sneak Attack Accuracy I-IV
Sneak Attack Training I-IV
Improved Bluff I-II
Improved Hide I-II
Improved Move Silently I-II
Rogue Wand and Scroll Mastery I-II
My reasoning on why other skills are not as optimal.
Extra Action Boost: You already get enough action boosts, I don't usually use them on trash as I save them all for the boss.
Action Boost Skills: Skills are already MORE than high enough. Increasing them further is useless.
Energy Resistance: 30 Resists are plenty good enough.
Dexterity Enhancements: Don't need it, way too pricy to increase a stat by just one.
Fear Resistance: Useless.
Heroic Companion: Useless.
Halfling Luck: Saves are already high enough, and the only one you really need to worry about end-game is reflex which is more than covered.
Halfling Skill: See "Action Boost Skills"
Halfling Thrown Attack/Damage: Useless.
Item Defense: Useless.
Faster Sneaking: I don't spend a lot of time sneaking, so no point in getting it.
Skill Enhancements: See "Action Boost Skills". While I do have two ranks in Bluff, that would be the only skill I'd really recommend. Even so, I wish I had something better so I could spend those AP elsewhere.
Trap Sense: Useless. Improved Evasion and I already only fail on ones.
Wand DC: Useless.