I have the CDS FASTA files for 3 organisms. I was wondering if there was a quick script, set of online tools, or methods to find the 3-way orthologs between these 3 organisms using the CDS FASTA files?
There are loads of options. For example, OMA and OrthoMCL are two popular software. You can look at MCL page under protocols for a quick how-to on clustering blast results - probably the simplest solution for you. You could also read old posts for suggestions, e.g. here and here.