How to align a chain on a single speed
To adjust chainline, you can:

At the back


use spacers between the hub and cog


At the front


use a longer/shorter bb spindle (as Kibbee says)
use spacers on the bb cups (as Mark W says)
use chainring washers (and likely different bolts) to adjust the position of the chainring on the crank


I'm struggling to think of any more options. 

The only other thing I could think of is that if you do end up with an imperfect chainline, despite your every effort, then a 3/32" chain will be more forgiving than a 1/8" chain. 3/32" chains are designed to be able to traverse cassettes so have a little more flexibility in them.