Are there any rules of thumb when computing pulse current ratings for PCB traces?
Ultimately this is a question of when the FR4 will reach maximum specified temperature of 135 degrees C given an etch dimension and current.  

The only analytical equation (that I've seen) that addresses time of heat rise of conductor given a current is the Onderdonk equation.  The equation is meant to cover heat rise to fusing temp (copper is 1083C). You can find a write up about it here on the ultracad site.  

I = \$\frac{A \sqrt{\frac{\log \left(\frac{T_m-T_a}{T_a+234}+1\right)}{t}}}{\sqrt{33}}\$  

or turned around:  

\$t_{\text{fuse}}\$ = \$\frac{A^2 \log \left(\frac{T_m-T_a}{T_a+234}+1\right)}{33 \text{ I}^2 }\$  

where A is circular mils, temperatures are in degrees C, and time is seconds.  

Be aware that the Onderdonk eq was written to estimate the time to fusing wire in air for a given current, not etch on a PCB.  Looking at its structure, it appears to consider only thermal conduction through the cross sectional area of the conductor (I don't see any surface area).  It is probably not accurate for times longer than 5 or 6 seconds, indeed for a long enough time zero current will reach \$T_m\$.  

Using the second form of the equation, 20Amps through a 50mil by 5.6mil etch would reach fusing temp in about 7 seconds and would reach \$T_m\$ of 135C in about 1.5 seconds.  These times seem shorter than expected.

It's a difficult problem and the thermal paths can have widely differing boundary conditions, limiting analytical solution region of usefulness.  You may get the best estimates by building some test boards and measuring.  

Note:  In my comment I mentioned a freeware tool at ultracad to calculate heat rise, but now see that it is no longer freeware.