My guesstimate:

* CD: Possibly the G98DH is somewhat better, hard to know if it will be audible.
* DVD: Picture quality/upscaling is much better in Oppo compared to G98DH, don't know if it will be noticable better than in the BDP-S500 though.
* DVD-A: The current firmware plays DVD-A, though it's still some work to do (mostly since about half of the existing DVD-A discs are "non-standard" in one way or another, mostly regarding menus). The G98DH can send it as bitstream and that would top what Oppo can offer.
* SACD: Does the Sony play SACD? Otherwise it's an easy win for Oppo, can send SACD out on analogue or HDMI (both DSD and PCM), and a modified Oppo will always win since it can go digital to the Meridian processor.
* Blu-ray: The picture quality would probably be equal for Oppo and Sony, but since you know only can connect audio from the BDP-S500 by one coax it's an obvious win for the modified Oppo since it gives you the HQ audio. The S500 would probably be more "mature" until Oppo has released one or two more FW updates (which they however usually are quick to do), I've read that a few DTS-HDMA discs have some glitches with the current FW.
* Other: You can connect a FAT32 USB disc to the Oppo and play some other formats, I believe FLAC is one of them.
* Support: Meridian and Oppo beats Sony hands down.

HD621, G98DH, G68ADV, Bc Acoustiqe ACT A3, 5200C DSP33, NuForce Reference 9 monoblocks, 2x SB3's, Velodyne DD-15 & DD-12 Subwoofers and a Meridian sub.