Rear triangle is out of alignment
 

I have a couple of frames with vertical drop outs where with the rear wheel in place, right behind the BB the wheel will be centered, but up by the brake bridge the wheel will be off center by a centimeter or so to the left if you're looking from behind the frame, does anyone have any idea how this could be straightened out? I'm just not sure which way or what side needs to be bent or how to go about doing this. One of the frames is steel, the other is aluminum which im thinking is a lost cause trying to straighten that one out.

Before you start grinding anything be absolutely certain that the wheel is fully seating itself in the dropouts if they are vertical dropouts. And if they are semi horizontal then equally be sure the axle is resting on the upper side of the slot. Also check the axle for uneven wear on the exposed threading as well as even protrusion. And check the dropouts for dings or divots in the saddle of the dropouts that could be holding the wheel out of alignment.

If you flip the wheel around it will tell you if there's some sort of minor rim runout or dishing issue or if the issue is at the axle or if it's in the dropouts. Also be sure that you use the same spot of the rim both at the BB shell and at the brake bridge so that you're certain it's not a rim runout issue.

+1 to BCRider's suggestions and also be sure you don't have a bent or broken axle.

+1,

This is the definitive test. A wheel problem will mirror when the wheel is flipped, a frame problem. If in doubt, borrow another wheel and reconfirm. I also confirm an axle issue by rotating the axle in the dropout with the bike standing on the floor.

This brings up a key point, always mount rear wheels with the bike on the ground, so gravity ensures the axle is at the top of the dropouts.

If you're 100% certain it is a frame issue, things get complicated, because it could be a bent (or badly built) rear triangle, or it could be dropouts at unequal heights. Before you can fix it, you have to confirm a correct diagnosis, and that's too long for me to explain here. If you think it's the frame, either see a knowledgeable dealer, or search frame alignment on the net.

You need to determine whether each dropout is the same distance from the centreline.

If the ally frame has vertical dropouts which are the same distance from the centreline, you can file one to make the wheel sit vertical.

If the right dropout is further from the centreline, you could dish a wheel to match the frame, but if it's the other way round it'd be pretty stupid.

...Obviously you need to ensure your wheel is true and dished with a straight axle before using it to try diagnosing the frame's condition.

I thought that there was a simple way to measure the alignment by using a string around the seat post and extending it to the drop outs. If it does not measure the same to each drop out then you have an alignment problem. This is probably harder to do than I think.

Maybe a long all threaded rod placed in the rear drop outs could be used to visually determine if the frame is not aligned.