Im running a 1000amp service using 3 runs of 500mcm in 3 runs each in 3-1/2 ridgit, what should I pull for a ground in each run?

You need each conduit to have a #2/0 copper or #4/0 aluminum, as per the National Electric Code 2008 edition:

(F) Conductors in Parallel. Where conductors are run in parallel in multiple raceways or cables as permitted in 310.4, the equipment grounding conductors, where used,
Shall be run in parallel in each raceway or cable. Each parallel equipment grounding conductor shall be sized on the basis of the ampere rating of the overcurrent
Device protecting the circuit conductors in the raceway or cable in accordance with Table 250.122.