I have a real cheap strat-esque guitar (SX brand) that I bought for $100 on rondomusic's website. I'm really close to just smashing it. Now I know it is a cheap POS, but I spent like 1-2 hrs tweaking this thing the other day and it just won't intonate properly. And when I say that I mean I have it intonated properly but it is still out of tune sometimes. It def needs new strings and I know that sometimes caused problems but I finally got the springs adjusted correctly and the intonation perfect according to the tuner but it seems that every chord is in tune but when I play the D chord it sounds like shit. The G and B strings are off. Do you think the neck is bowed? thats the only thing I haven't checked and thats only because I've never messed with that before, but I guess a $100 guitar would be perfect for practice ;-)
Tuning/intonation is always an issue with cheaper guitars, but as a rule it is always a compromise with guitars, too. All tuning methods are a compromise, and you shouldn't rely on a tuner except in loud/stage situations.
Here's a listing of some of the more popular tuning methods: http://www.truetemperament.com/wp-content/uploads/2014/04/Tuning_Methods_Evaluated.pdf

Personally, I use a variation:
Tune the A string to a tuner. This is my base reference point.
Play the 5th fret harmonic on the A - this is a 2-octave A, play the 7th fret harmonic on the D string and tune the D string to match the harmonics.
Play the 12th fret harmonic on the A string - this is the octave A, play the 2nd fret on the G string and tune it to the harmonic.
Play the 12th fret harmonic on the D string - this is the octave D, play the 3rd fret on the B string and tune it to the harmonic.
Play the 7th fret harmonic on the A string and the 5th fret harmonic on the low (1st) E string and tune. Same note is the open high E (6th string).
There are similar variations, and some willwork better for some guitars than others.

Before you try all this, change your strings, give them a stretch, then tune up and reset your bridge intonations based on the 12th fret harmonics/played 12th fret notes.

usually the G and B strings will be the 'culprits' in bad sounding tunings, and depending on the guitar going to a thicker gauge string helps.
My reverbnation page

2012 Taylor 310ce
2011 Fender CD140SCE
Ibanez 12 string a/e
73 Epi 6830E
72 Fender Telecaster
Epi Dot Studio
Epi LP Jr
Chinese Strat clone
Washburn Mandolin
Luna 'tatoo' a/e uke
antique banjolin
Squire J bass