What methods do you use to arrange songs?

I've been coming up with lots of good riffs, tunes, and the like recently, but am having serious trouble stringing them into coherent tracks. I feel like a guy with lots of Lego bricks but no instructions. I could follow a clichéd route of intro-verse-prechorus-chorus-repeat-break-end, but that gets obvious very quickly. For example, how do Opeth come up with those almost-random progressions? Coming from the other extreme, what do you do to prevent a non-repetitive song from just being one long chain of unrelated sections?

I'm interested to hear what other people are doing in this regard.
 
Opeth is almost a 'jam'. They play for however long they think sections should go for. When it's time for a change they change. That's how most music goes (um, good music. ie Metal, Prog, etc)..

Just do what you feel. Play a riff for however long until you think "it needs some variation or a change there", then change it. That's what I do.
 
Well, yeah, I have a good idea of when a section has outlived its welcome, but then what? I'm trying to get an idea of how people decide to arrange these sections, and merely placing 5 minutes of unique parts in a sequence doesn't really satisfy.

Let me put it another way: I already highlighted one clichéd way in which you can construct the typical pop/rock song. In classical music you have things like ternary or rondo form, describing how the different sections relate to each other. Maybe I should just write a melodic-death track in Beethoven scherzo form and see if anyone notices. :)
 
If I come up with a riff and I would like to add onto it, I usually estimate the key then work with the notes to see what I come up with. I really don't arrange into intro-verse-bridge-chorus [ect.] form but I'll have 3-5 different riffs and play each until I feel like changing. Most things I write are built around a solid keyboard "riff" so the bass follows what I play with my left hand and guitar or alternate bass plays something similar to what my right hand would play on the keyboard. I haven't come up with a system for writing lyrics, since I generally suck at it - but I try to stay with the black metal style of writing a long poem with no definite parts.
 
I've been coming up with lots of good riffs, tunes, and the like recently, but am having serious trouble stringing them into coherent tracks. I feel like a guy with lots of Lego bricks but no instructions.
Well, the first thing you should do is to get to know what certain Lego bricks are made for, right?
It is more obvious in rock and hard rock music. Every part of the song has its own function. It can raise tension or it can resolve the tension, it can lift you up, or it can chill you out.
In usual hard rock song structure can be quite simple

Intro - It makes you interested in song and puts you in certain mood before song begins. Intro can be just an effect ranging from screaming to sounds of rain, to some simple melody part, but the function is the same.
Riff - It is repeating part that should be hooky and have a lot of tension, usually something memorable enough. Sometimes it is not a riff but melody played on instrument with riff underneath it.
Verse - verse tells the story of a song, usually it is not too much melodic (it depends) because you don't want it to be stronger then riff and more "up" and hooky than chorus. Sometimes it is same as the guitar riff from the beginning, ir variation of the same riff, but with vocals.
Bridge - sometimes it is there, sometimes not. Its function is to lead in to chorus, to build up tension, often there is some difference in chords voicing compared to the rest of the song. It is different than verse and chorus
Chorus - Usually most important part of the song in rock music. It is biggest happening in the song, and it is telling message of the song lyrically. all that has been said in verse is condensed in a small number of words, that are easy to remember and eventually sound strong. It can be also build on riff, but with strong vocal part over the guitar riff, and then after the end of the chorus, guitar riff continues without vocals or song directly goes to another verse. In heavy metal and modern rock music, things have changed a bit, so sometimes chorus can be a most "down" part of the song, and strongest part of the song can be a riff and variation of it in verse. And sometimes there is no chorus.
There can be other parts in song, like outro, another different bridge before the solo and guitar/keyboard solo part, outro, etc.In a Dream Theater song you can have a lot of different choruses bridges and riffs but they have similar functions like it is a 3 minute simple song.

So what are musical tools to make parts build or resolve tension in HM music? Changing drum patter to halftime and back from part to part. Adding or removing another melody from the basic riff or part. Making variations of the same part for verse and bridge or verse and chorus. Adding frequencies that are missing in one part to another part, for instance, you can have only a vocal and very low down tuned riff in verse, and then for another part adding very nervous midrangey melody over it. Or adding something that is high pitched. Also by making variations in rhythmic and melodic structure of vocal or singing stile from part to part.

You need to have in mind that is easier to understand and learn arranging by listening to some contemporary, older and more simple music, because it is all more obvious there. Then you can take that knowledge to more complicated and alternative forms of metal. It is based on same principles, but they are a bit less visible in Opeth song than in some Iron Maiden or AC/DC tune.

By not just listening, but analyzing structure of the song you like, you can learn how they are built, there are some laws and rules in arranging and composing that you can grasp that way.