AOT node compare
One of the most often used tool is the AOT node Compare utility, which has some improvements from the past but can be changed further.
Now in AX 2012 the compare tool can be executed as CIL code rather than in the X++ runtime tier, which should give you considerable performance boost for larger code comparison. Here is a great post (The compare tool–and running X++ code as IL) from mfp about improvements that Microsoft did.
On the other hand you can do some improvements yourself by adding the following line to the SysCompare class, selectionChanged method: