S.P.E.C.I.A.L:
Strength is for if you want to be melee, unarmed, large weapon focused or enjoy hoarding loot. 6 is good or most weapons, 8 is ideal if you want the largest or melee/unarmed focus.
Perception sounds useful, but is less so if you like companions (ED-E for example as others have mentioned). Basically if you want to go solo then it is better to be higher, otherwise not so much.
Endurance is for health, resistances and toughness, if you want to get into the thick of fighting you want it to be 7+.
Charisma is worthless unless you want to be a smooth talker or have companions buffed up. If that kind of thing is your style then it is good to have it high.
Intelligence gives you more points per level which is why so many recommend it. If you want to max skills then it is a good way to go, but it really isn't "needed".
Agility helps with stealth and makes you harder to hit. Very useful for sneaky and close combat types, not so necessary if you are dragging around big guns.
Luck helps with criticals both yours and reducing the chances of the enemies getting them. It also raises all skills slightly and helps with gambling.
Overall on a first go, I'd recommend keeping them all at 5 and just raising some in the areas that seem to fit your style.
Skills:
Tag the three skills that you think you will use the most. I recommend at least one attack skill such as Guns, Energy weapons, Melee etc. One passive skill such as Speech, Medicine or Repair and one technical skill being either Lock Picking or Science.
That will make you nicely balanced. Most skill points when levelling should go into those, with the occasional points elsewhere for perks.
Perks:
Whenever you level up keep an eye on what is required for each perk. Make sure to invest skill points in those areas so you can get the ones you like. As for what to go for? Just read them all when you level up and pick what you think seems cool, don't worry about "optimal" builds on a first run.
Just my two cents. I prefer to not try and get the "best" build on my first play through as it is more fun to experience it and learn what works for yourself.