Disclaimer: I'm playing GOTY and so I'm assuming Broken Steel in all the following text. If you don't have broken steel then pretend my post doesn't exist. It does not pertain to Broken Steel-free environments. Also, the opinion expressed in this post is exactly that, an opinion. It is to be considered a WIP to be debated rather than cut-in-stone suggestion of fact.
That being said, I'm really not an expert at this point, but after studying the mechanics and the perk list a bit, I end up with the following as largely optimal for a fairly sneaky small guns specialist.
S P E C I A L5 6 7 1 9 6 6
These values are largely based on the desired perk selection.
Perk SPECIAL requirements:
Spoiler
Strength
4: Little Leaguer, Iron Fist
5: Strong Back
Perception
4: Thief
6: Sniper, Light Step, Better Criticals
7: Infiltrator
Endurance
5: Lead Belly, Toughness, Rad Resistance, Size Matters, Strong Back
6: Life Giver
7: Solar Powered, Rad Tolerance, Rad Absorption
Charisma
4: Child at Heart, Scoundrel
5: Impartial Meditation
6: Animal Friend, Master Trader
Intelligence
4: Daddy's Boy / Girl, Gun Nut, Swift Learner, Comprehension, Educated, Entomologist
5: Nerd Rage
7: Computer Whiz, Warmonger
Agility
4: Gun Nut, Thief
6: Sniper, Silent Running, Light Step, Action Boy / Girl
7: Nerves of Steel
Luck
5: Fortune Finder, Scrounger
6: Mysterious Stranger, Better Criticals
Red = Complete crap that it's fairly hard to imagine you'll want.
Blue = VATS-related perks that are just about useless to heavy weapons specialists.
Essentially, a sneaking small gunner will probably invest in VATS and thus be interested in Sniper, Action B/G, Silent Running and possibly (though I personally wouldn't be) Mysterius Stranger. This means PE, AG and LK at 6. If you're really VATS-addicted, you might consider Nerves of Steel, but from the description it doesn't seem to do much at all. Strong Back is a must for anyone interested in carrying loot around, so that's 5 ST and EN minimum. Toughness is also fairly awesome so make that 6 EN minimum. CH perks are useless so all you need is 1. Despite hitting level 30, you'll probably still want Comprehension so 4 IN is minimum.
Essentially, there really aren't any good perks that require more than 5 strength, 6 perception, 6 endurance, 1 charisma, 4 intelligence, 6 agility (maybe 7 for Nerves of Steel), and 6 luck. That totals out to 34-35 points, leaving you at least a further 5 for specialization. If you skip NoS then 6 agility will do, and you've got 6 points to spare. +5 for intelligence + early bubblehead gives you maximum skill point freedom and that rocks. That leaves 1 point, which I'd throw into endurance. Not because any of the perks are really worth it, but because more hitpoints is nice and it makes it easier to complete the Wasteland Survival Guide with the damage resistance option. Only alternative is luck, which would mean +1 initial base of all skills and +1% chance to land a critical. That leaves us with...
S P E C I A L5 6 7 1 9 6 6
It may seem odd for build relying on sneaking and VATS to only go with 6 agility, but remember how important skills are. 9 base + early bubblehead means 20 skill points from levels 3 through 30. Combine that with Comprehension and you'll be able to easily max all skills and have plenty of room to spare for "inefficient" skill point distribution. Effectively, we're talking 28 *20 = 560 skill points from levels, 25 * 2 * 13 - 2 = 648 from books with comprehension, and a further 130 from bubbleheads. Add Almost Perfect to the mix (and thus potentially a perfect 10 in all attributes) and all skills will eventually baseline at 25, or 27 if you go for a perfect 10 in everything. That means you only really need 75 * 13 = 975 points, out of the 560 + 648 + 130 = 1338 you've got available. In other words, feel free to boost repair, speech, sneak, lockpick, science and small guns (and maybe even barter) to 60 before books and bubbleheads. "Wasting" 20 points on 7 skills really just means you've got about 1200 skill points out of 975 needed.
The above is specifically for a small guns user, however. What if you're into energy weapons? Well, that really shouldn't make any difference. More expensive approach in terms of caps investments required, but not heavier than small guns and very viable for sneak and VATS.
What if you're into heavy weapons? In that case you probably don't give a toss about VATS and really shouldn't worry much about agility anyway. Dropping agility to 1 gives you 5 points, which means you could put 3 more in ST (reaching 8, +1 from Those! and +1 from bubblehead) and 2 more in EN or LK (or 1 in both). Why do heavy gunners need more ST anyways? They don't except if they want to also move around. Heavy armor weighs a ton and the same applies to the weaponry. Thus, more ST = more room for loot = more caps to spend on the crazy amounts of ammo swallowed by your minigun, gatling, or whatever. How about EN? Well, if you're not sneaking around, there's a good chance you'll be hit more. More EN = bigger tolerance to being shot repeatedly. The compromise between LK and EN may be better, though. +1 LK gives +1% crit and +1% all skills. A further point merely gives another +1% crit whereas +1 EN would've given +20 health and +2 big guns skill.
Obviously, one might also decide to not give a toss about PE. It's only good for adding enemy markers to the compass, after all, and you'll probably get those anyway when something attacks you. If you decide to skip the Better Crits perk then there's no reason not to invest more heavily in luck. Heck, you could even drop PE to 3 and max out EN while you're at it.
S P E C I A L OR S P E C I A L OR S P E C I A L8 6 9 1 9 1 6 8 6 8 1 9 1 7 8 3 9 1 9 1 9
As for melee and unarmed, I will need to try those skills more extensively before making any serious comments, however I'd guess that it's largely the same as heavy weapons, max ST and EN and then to hell with AG and CH.