This is a good one. Let's see:
Dragon Rampant has already been mentioned, but you can fit the figs into all sorts of skirmish and small-army fantasy rules. Song of Blades & Heroes springs to mind, and you could fit them into the 5150 rules sets with some effort. I remember discussion about stats for the Ares rules from Majestic 12 but that was years ago, maybe even pre-Hordes. Armies of Arcana might work too - Privateer armies would tend to have low model counts but high quality compared to the more normal AoA lists.
The 'jack side of things ought to work in any VSF game (IHMN was mentioned) as well as various pulp adventure rules (.45, for ex). The hordes range is super useful for all sorts of fantasy and horror RPGs, as are the Cryx and Cephalyx minis (who doesn't love mechanical undead and mad science?). And you could easily adapt the Goalsystem rules (Supersystem is probably best) for them. GS is built around small skirmish fights full of models with weird powers and small squads of scut troops who die like flies - it's practically perfect for WarmaHordes ports, and has a robust and versatile design-a-fig (or squad) system built right in.
Kudos to you for looking for more uses for the Privateer figs. I've always considered it a shame that they don't see wider usage outside their parent rules.