I've been using Stuffit Deluxe 3.0.7 under System 6.0.8 on my SE/30 for ages now, although I must admit I don't use it that much at all. I use Stuffit Expander 5.5 more frequently, when running under System 7 or 8 on my SE/30.

Interestingly, this Macintosh Garden page says that Stuffit Deluxe 4.x should work under System 6, but I myself have not tried it. You therefore may wish to post your experiences in the comments section on that page.