Rear wheel not centered between the seat stays makes setting up cantilever brakes a bitch.

My rearwheel isn't centered between the seat-stays, I've tried different wheels and also tried putting it in the wrong way around (i.e. cog on the non-driveside), didn't change anything so I'm pretty sure my drop-outs aren't centered. It's an aluminum frame so I don't think I can fix that? Would my best bet be a janky rear-brake set-up or is there something else I can do?

Does dishing help if dropouts are out of line?

You could take a file to the drop out and enable the axle to take a position that ensures the wheel is lined up at the brake. However, if you wanted to take a more longterm view, you could check the frame to see whether it's true (see Sheldon Brown's piece of string method for that) and also check that the drop outs are aligned (probably need yer LBS for that unless you have the right tools). If there's something seriously misaligned with the frame, then I'd be thinking about changing it - bent/crashed aluminium will have lost a lot of strength and could fail.

Track ends or vertical dropouts?

Wheel even between the chainstays?

You could try fixed-wheel?

String method shows it's slightly out of true, seat tube is 3 mm closer to the drive side. :\ So I guess the frame is wonky and I can't fix that.

I'll just set-up my brakes as good as I can and keep my eyes out for a new frame. I checked the frame for cracks in the paint and other anomalies around the welds but didn't find any so I'll just hope it won't fail on me until I can afford something better.

Vertical dropouts, seem to be even between the chainstays but can't tell for sure because they're asymmetric for crank / chainring clearance.

I suppose re-dishing could fix it, but the wheel is centered and I'd rather keep it like that. I'll just replace the frame as soon as I can.

I guess fixed gear cyclocross would be pretty rad, but not the solution I'm looking for. ;)

Defo sounds like the frame has taken a hit. Filing one dropout would fix it but as said above, if wonder what had happened to make frame be like that and what that meant about its integrity.

Quite possible that the frame was built like that ...

Do the brakes have spring tension adjusters? Can you use that to adjust the arm position? Is the pad position adjustable relative to the arm? If it uses pads with a smooth shank this should be fairly simple, if it's screw- on pads you might have to play with adding washers as spacers.

I'd not be inclined to redish the wheel to try to solve it. Filing the dropout might help - you wouldn't need to take much metal off - or it might be that there's a bit of crap caught in there.

Try it - it's really rewarding (some podium finishes in Denmark by a guy riding fixed gear CX)