It's amazing how many people have chimed in here. Honestly, I never expected this to grow like it has. This site and others like it have given me many insights and much good advice, so I was just trying to give back a little. I'm glad I've been able to do my part.
To your questions... The EAH4550 has several pros, and several cons, vis-a-vis the MSI 8500GT. On the plus side, the biggest advantage for me is better video playback. Every movie plays absolutely silky smooth. No frame skips, no lag, no stutter. I didn't get this with the MSI 8500GT. Some movies would play well, some would only play well under ArcSoft TMT, some under PowerDVD, some not at all (see my earlier posts about ID4). With the EAH4550, it doesn't matter the movie or the application, everything plays perfectly.
The downside is audio handling, although the EAH4550 should have a major leg up here. The MSI uses an S/PDIF passthrough to get the audio onto the HDMI bus to your playback device(s). So, you're limited to Dolby Digital EX or DTS-ES as the most defined audio sources. TrueHD and DTS-HD will not go over S/PDIF, as it doesn't have enough bandwidth for those formats.
The EAH4550 has it's own, built-in audio processor, that is (according to specs) capable of encoding TrueHD and DTS-HD on the card, then shoving it out the HDMI. In theory, this would make it the obvious choice for audio purposes.
The problem is... I can't get the darned thing to work! I've detailed the issues I'm having in detail, and so far, although a lot of helpful souls have offered suggestions, none of them have worked. I am still using the z555's onboard audio, going out the optical TOSlink connection. I honestly think at this point that it is a limitation of the chipset or motherboard, and the device just will not work due to the (relative) lack of resources on the mobo.
So, which is better?
Video playback: EAH4550.
Audio compatibility: MSI 8500GT.
Low noise: Tie (the MSI 8500GT is passively cooled, the EAH4550 has a fan. But you can't hear it over the other fans in the z555.)
Driver support: EAH4550. (I've always been an nVidia fan, but I have to hand it to the Catalyst folks, they know their stuff.)
Case Integration: EAH4550. You have to remove the VGA plug with the MSI card. That's okay, you use the hole for the S/PDIF cable to go from the coax plug on the back and inside to hit the card. But the EAH4550 has no need of this (in theory) and comes with it's own VGA plug, which can go back into the hole in the case. Better looking setup. In either case, you'll have to do a bit of metalwork, at least bending and tugging, to get a low-profile bracket to cover the card, unless you carve up the stock one with a dremel.
For a BD/HD/DVD drive, I'd still go with the LG dual-format. I haven't found a disc yet that it won't read or burn. Mine is the GGC-H20L, which means it only burns DVD+-RW, and DVD-DL. The GGW-H20L is the one that adds Blu Ray burning, so I can't speak to that.
It comes with PowerDVD 7.5, or did when I bought it. The funny thing about PowerDVD is this. When it came out, the OEM version that came with the drives didn't get the same updates as did the retail version bought separately. However, once Cyberlink released version 8.0, they seem to have put all the updates available for all to use. Now, PowerDVD 8.0 removed HD-DVD capability, but PowerDVD 7.5 properly updated plays all my movies perfectly. ArcSoft TMT works as well, and the latest versions still support HD DVD as well as Blu Ray.
Since your PC has the same chipset as mine, I can verify that the Pentium 4 650 (3.4 GHz) will work. Some have reported getting the 660 and 670 to work, but I cannot confirm this. They are made on a different manufacturing process than the 650 and back, so that's a risk if you go that route.
I wouldn't think that the mobo would fit a new case. They were custom designed by Asus for the z555 series, and most of the plugs wouldn't line up with anything I'm aware of. If you go for a new case, then I'd suggest selling the z-machine on Bay, and using the proceeds for a new mobo/CPU/RAM. You'll break about even (z552->internals) and the performance will be a lot better. I keep my z555 because I like the aesthetics, but if I were to want a new case (bigger PS, different look, etc.) I'd change the internals, too. The z555 series is just too dated to keep around in that circumstance.
Having said that, I'm going to keep it until it literally flames out on me, and THEN get a new machine. But the point has been the modification process. Like putting a supercharger on a dated car, it has really, really increased the "fun" factor of the machine for me, and I'd wager a decent percentage of the folks here.
Good luck, and if you do work on it, post up so we'll be able to help, or celebrate your results!