My Wanhao Duplicator i3 had a few frame alignment issues but nothing major. I found the frame where the Z-axis motors are would touch my table surface and the Y-axis frame would rock slightly (2-3mm) pivoting on the Z-axis frame pilars. If your frame is seriously out of align then other remedies will be needed, but the next part of the description has really worked for me.

Fitting feet to my frame improved this issue massively and made the whole frame feel very solid. I used a spirit level across the 2 Y-axis linear rods to level the whole printer, both back and front. Before this my hotbed springs were very misaligned in-order to get the hotbed glass flat and tuned to the X-Z axis gantry. These are the feet I am using
http://www.thingiverse.com/thing:1370173
After this alignment and a few other additions (see my other uploads) all the hotbed springs are almost identically aligned and bed trimming is easy and not necessary as often.

So this brings me to this new part, its a clone really of a design by Mangtronix http://www.thingiverse.com/thing:280974 but after printing his part I found it wasn't long enough for the Wanhao Duplicator i3 (I didn't realize at the time the original is customisable), so I made a new one.

Assuming your Y-axis rods are 100% level (or as good as you can get), this then allows you to align the X-Z axis gantry to the Y-axis. Works very well for me and seems the best place to align from, as the sheet metal frame of the Wanhao is not level in most areas.

For alignment I did the following:

1) I moved the X-Z axis gantry to a suitable height using the control panel or manually.
2) Turn the whole system OFF from the mains
3) Disconnected the Z-axis motor connections
4) Move the Y-axis all the way toward the front of the printer
5) Fit the alignment bars to the Y-axis as shown in the images
6) Manually turn the Z-axis motors down until they make firm contact with the alignment bars. ENSURE THE ALIGNMENT BARS ARE SQUARE BOTH SIDES, TO ENSURE THE BEST ACCURACY.
7) Then connect the Z-axis motors again (make sure your system is off before doing this)
8) Power the system back on again
9) Move the Z-axis motors up and away from the alignment bars using the positioning system via the on screen menu.
10) Remove the alignment bars and your done!