I think the number of visible markers in D. melanogaster is often under appreciated by fly researchers. It really only became an issue for me once I started stepping out of D. melanogaster and started looking for markers in D. simulans and more recently D. pseudoobscura.
The marker that I utilized in D. simulans was a GFP insertion (Castillo and Moyle 2014, creation of flies explained by Holtzman et al 2010) because it was dominant and could be seen in F1 hybrids.
For D. pseudoobscura there are also GFP insertion lines, but for my work with D. pseudoobscura I ideally wanted to complete sperm competition assays between wild type genotypes (and not a standard lab genotype). My solution was to introgress this GFP marker into several isofemale lines. Luckily D. pseudoobscura has ~6X the recombination rate of D. melanogaster, which would allow quick introgression. The down side is the large inversions on the 3rd chromosome.
I decided to map the GFP insertions using a strain that is marked with visible-recessive mutations on all of its major chromosomes. If the GFP did not co-segregate with any of the mutations then I would have determined which chromosome the insertion was on. Below I share some of the phenotypes I was scoring in the backcross generation:
The back cross individuals were all yellow (X chromsome) and segregated for gl (glass eye phenotype) and or (orange eye color) with an appreciable frequency of double mutants. They also segregating the GFP insertion. Starting in the upper left corner and moving clockwise we have gl/gl;+/+, then +/+;+/+, then +/+;or/or, and lastly gl/gl;or/or. In the second picture (same flies but they have moved around some) you can clearly see the GFP insert in the +/+;or/or fly and it is also visible in the wild-type fly (its even easier to view in the ocelli). This indicates that the GFP insertion is on the second chromosome as it is never found with the gl marker.