Depends on which d20 game I'm playing, mostly. For Cthulhu we don't use anything. For most others, we usually use a battle map with a combination of specially printed counters, prepainted D&D minis, unpainted or manually painted minis from other sources (Warhammer, Reaper, Warmachine, Rackham, etc.) or whatever's on hand, including spare dice.
I'm sure we use more of the D&D minis than anything else, but that's not exclusive. Often I like to use a specially painted mini that I have, and I sometimes even have to prepare monster stats that specifically match it. At my session last week, I used four WH40k termagaunt minis, for instance. Made up some stats on the spot. If I'd been more on the ball, I might have used kythons from the BoVD. Point is, I occasionally let minis drive the action rather than the other way around.
In theory, I'd prefer play without minis, or any tactical battle representation at all. I don't actually much like dropping out of the RPG and into the mini tactical game. But d20's other benefits lead me to ignore that most of the time.