I forgot that Poggle is also still in custody after the Season Two Geonosis arc. San Hill hasn't appeared yet, so it's unknown what his status is.

Leland Chee said this on one of his Chronicling The Clone Wars blogs:
Nute Gunray’s escape while en route paves the way for his appearance in future episodes in the series and in Revenge of the Sith. Other Separatist leaders who get captured during the series only to later appear in Revenge of Sith won’t fare as well, spending much of the time span of the series in incarceration.
So hopefully their fates will be resolved in the series.