Here's what I did.
1) Check to see if your latest LSAT is above the school's 75th percentile.
2) Call or email the admissions contact for that school and say that you're interested in applying and would like to request a fee waiver.
3) Comply with any instructions they give you in order to obtain one. They may want you to email their admissions office.
4) If they tell you that it's going to be a while until they send out the next round (Vandy did this), ask if you can get a projected date on the next round of fee waivers. If the fee waivers won't come out until after Jan. 15 or so, you need to make a decision: is a greater chance of admission worth applying now and paying the application fee? (Answers: yes for reaches, especially those with small class sizes; maybe for targets; no for safeties.)
5) Thank the adcomm for his/her time.
Note that Emory and GWU will not grant merit fee-waivers, nor will HYS.