Disease gene identification techniques often follow the same overall procedure.  DNA is first collected from several patients who are believed to have the same genetic disease.  Then, their DNA samples are analyzed and screened to determine probable regions where the mutation could potentially reside.  These techniques are mentioned below.  These probable regions are then lined-up with one another and the overlapping region should contain the mutant gene.  If enough of the genome sequence is known, that region is searched for candidate genes.  Coding regions of these genes are then sequenced until a mutation is discovered or another patient is discovered, in which case the analysis can be repeated, potentially narrowing down the region of interest. 
The differences between most disease gene identification procedures are in the second step (where DNA samples are analyzed and screened to determine regions in which the mutation could reside).