I'm somewhat biased when it comes to "Son of Thunder" because it was my first Scratch purchase (high school). It's a cheapo 2-disc comp on some random label but the sound is good and it includes many of my absolute favorites including "People Funny Fi True", "Bucky Skank", "Bathroom Skank", "Soul Man", "Yakety Yak", "What A Botheration", "Cow Thief Skank", "Kentucky Skank" and "You Crummy". If you're unfamiliar with these, definitely check em out. Most seem to also be included on those Trojan Upsetter singles comps (which are chronological and also include the dub B-side versions) which seem to be really great as well. Only heard one of them (vol. 4 I think) but if I had to do over again, I might grab them all.
Aside from "Son of Thunder", my favorite random Scratch comps are "Dry Acid" (early stuff- late 60's), "Give Me Power" (more early stuff), "Voodooism" (later stuff, weird n' eclectic) and the 2-disc "Anthology" which is the best overall summary of his career I've found. "Arkology" seems to be the most popular and there's great stuff on there but also some mediocre stuff and a lot of the best tracks are from those classic albums he produced for other artists, which every reggae fan should have anyway.
It also depends on the era. Desmond was sort of in the pre-album era for Jamaican music so his albums tend to be cobbled together, making comps more appropriate. Generally I feel you though- best to get individual albums rather than comps ("I See You" is the main cut I miss from the '75 version of "Funky Kingston" but same difference). And hey, hit me up if you ever make it out to SF.