Okay, up until now I've just been learning other people's music, I've tried some of my own stuff but nothing particularly great has come of it.
How do you guys come up with your rhythms?
And how do you apply scales to making music, for instance the pentatonics (picked this because it's easy), I've heard a lot of songs in pentatonic and when I look at the playing of them I can see how they fall into pentatonics - However, they're not in box patterns or anything like that, where did the artist come up with the idea of where to go?
Would this mean it's NOT a good idea to learn certain formations of scales? Would it be better to just find all the notes that fall within that scale on the fretboard and go wherever you like with it?
it just has to come man..

i cant explain it...i can give you an explanation actually,but if you follow a procedure the song wont be amazing

the best songs will be something creative

so for instance take some random chords and a lick here and there from the penantonic and stuff...

or mix the penantonic scale with other scales like the natural minor and youll get somethign cool
Fender Stratocaster,Yamaha ERG 121 and 5 other random low budget acoustics
Finding a good rhythm for your songs can be quite a challenge, sometimes it's even harder than finding a melody. The trick is to tap your foot, bang your head, "play drums" on your lap until you find something catchy. It also depends on what style you are writing. If you are writing metal, listen to some bands like Children of Bodom, Necrophagist, or Nile for ideas. Classic rock, try Boston, Led Zeppelin, or Cream. Analyze what techniques they use to get their sound.

As for using scales to make music, scales are nothing more then a set of notes played in a logical order. Taking a look at a Major or Minor scale can help you figure out what notes are in that particular key, but just playing up and down or randomly picking notes from a scale probably won't be the most musically-attractive choice.

One thing I've found that helps me is to hum a melody or solo. Sometimes while I'm at work (like I am now) I will think of great melodies. Another approach is to listen to a pre-written song, and hum a melody over that. Say you hear a song and you think of a great melody that could go over it. Write another song in the same key, and use your melody! Or, transpose both the chords and the melody to a different key.

Just play a simple chord progression, G/C/D/C perhaps, and record yourself playing it over and over. Listen to the chords, feel them, and write a melody over it. This is a great drill to improve your melody writing.