Not sure why some people are so fond of the Good Natured trait- so it adds a small amount of points to several miscellaneous skills (none of which are sneak or weapons skills), but you'll easily and quickly gain all of those points you care about anyway, simply by using the skillpoints you get as you level up normally. I've never taken Good Natured, and I've always ended up with as many points as I wanted in each of those skills, well before reaching 30. Its downside is that it steals a trait slot that could be used to actually improve your character's capabilities throughout the game, in ways that a small handful of early skillpoints cannot. Oh, and it also gives a skillpoint *penalty* to guns and explosives... bad.
But anyways... stealth character? Not much in the way of extra things to get that will directly affect your ability to be sneaky, other than Silent Running (best perk in the whole game, bar none), and getting silencers on your weapons of choice. Put plenty of points into Agility and Luck, for improved sneaking, guns expertise, and weapons crits. If you're killing from stealth, you want as many one-shot kills as possible. Along those lines, the Commando, Sniper, Finesse and Better Criticals perks are all recommended. Unless you want to be a close-in stealth killer, specializing in pistols- then go with Gunslinger and The Professional, instead of Commando. Or do both, for plenty of options. And of course it should go without saying that you'll want to get guns and sneak up to 100 asap.
Armor? Always stick with light armors- medium and higher make you less stealthy- enemies will see and hear you sooner than if you wear light armor. Reinforced leather is some of the best you'll find early on- but the best I've found yet is the Vault 34 light security armor- it gives you 16 DT and only weighs 15 pounds. You can find 3 or more of them in that vault, when you clear it. Save them and repair to full durability. Also remember to keep your companions stealthy too, wearing light or medium armor- it doesn't help to be stealthy yourself, if your companion is clunking around in heavy combat armors. I'm not 100% sure how your companions factor in as far as stealth and being spotted by enemies works... but I've always erred on the side of caution anyway. If what your companions wear doesn't factor into how easily your party is spotted, then I'm sure somebody more knowledgeable will come along and enlighten us.
Weapons- silenced 9mm, 10mm, and later on the 12.7mm pistols, as you can get them (I use expanded weapons mod, so not sure if all the silencers I mention here are available in vanilla, or not). Rifles- Ratslayer is priceless- may not have the punch of a the big rifles, but it'll do one-shot kills on 90% of the mobs you'll encounter, throughout the game, even once you hit 30... and ammo and repairs are dirt cheap. Sniper Rifle, and the Gobi Campaign rifle (elite sniper rifle) are the heavy hitters. Some like the elephant blaster (Anti-Material rifle), but it's expensive, ammo is very expensive, costly repairs, gotta have 8 strength or 6 strength and waste a perk on Weapons Handling... etc. And no silencer! And as heavy as a small SUV. I never have bothered with it. And if you get the WME (expanded weapons mods), you can get silencers on other weapons too- most notably, the marksman rifle/All-American. When silenced, that weapon nicely fills the gap between pistol range and heavy sniper rifle range... good sneaky midrange weapon.
Also, for a secondary specialty, I like to go explosives. Always handy in a pinch, especially when you come across gaggles of enemies that are all clumped up in a tight bunch, or in a room around the corner, etc... where a tossed grenade is an easy 'final solution', and sneaky sniping isn't practical or is too dangerous. Especially since the last patch, explosives are a good all-around weapon to have, and even better when buffed up. Sometimes, the best silencer is a handful of TNT! You don't have to worry about an enemy alerting his buddies, if he and his buddies are all wall art.
If you have all of those things covered, building and playing a good stealth-based character is actually more about attitude and skill and experience, than skillpoints and perks and gear. And there ain't no better way to be good at it, than to go out and do it. Also, if you find your companions screw up your sneakiness too much, you may want to park them before going into combat, in a lot of places. Have fun!
PS: These tips are based on a stealth/killer build... if you intended to be more of a stealth/avoid conflict/pacifist type, then most of this won't apply