Wow, all those are great questions. I'll do my best to answer them all as clearly as I can.
As far as perfect emulation vs. good emulation. This is obviously an opinion. It's like asking someone what their favorite color is. Mine's purple, but you may wrongfully disagree if you like

So here goes, IMHO
S-Video out to a TV and Windows MAME
(1) great looking emulation but not perfect
(2) very affordable and easy setup to get running.
ArcadeVGA on a 15kHz 19" arcade monitor.
(1) a nice way to bring an arcade cabinet to life, vsync is perfect (which is always nice)
(2) solid 3D / 2D performance that allows you to run things other than MAME on a cabinet.
(3) I imagine games look pretty damn good, though some may not be perfect.
(4) fairly easy to setup and get running.
Trident Blade T64 or ATI 7500 with AdvanceMAME on a D9200
(1) perfect emulation.
(2) requires Windows9x or linux (NT support is experimental)
(3) this setup is pretty much for the MAME enthusiast and requires a decent amount of technical knowledge.
(4) expensive, especially outside of the US.
Setups I don't care for too much
Windows MAME on a D9200 or PC monitor
(1) I prefer the looks of a TV.
(2) waste of good money.
Is this something that is noticeable on 5 games out of 3000, or does it affect a majority of the games available?
Well, you ask a great question here. Most of my friends can't see the difference between any of the above setups, except, of course, the PC based ones!! So how noticable is it? I guess this just depends on how good your arcade gaming memory is. All of the above setups are pretty much great, though there are subtle differences between them all. Many I talk to can only see the differences once I point them out. So I don't know what to tell you here. My favorite is obviously the one I run, but Windows MAME on a TV is a great looking, cheap, and easy alternative. As far as ArcadeVGA goes, I know a lot about arcade monitors and AdvanceMAME, so it really doesn't do much for me. It's great, though, for those that want an AdvanceMAME setup, but who aren't interested in all the technical nonsense that comes with getting one up and running. Basically, it makes all the comprimises for you, which it does a very good job of, in my opinion, especially on 15kHz arcade monitors where there are a lot of comprimises to be made. On a D9200, however, many comprimises can be thrown out the window, so they aren't as important.
As I see it, it allows for 640x480 & 800x600 resolution in addition to the standard arcade monitor resolution, meaning that games look good and Windows looks good.
Technically speaking, it should look the same, but I couldn't personally tell you, as I haven't tested it myself.
Since I do plan to run this thing in a Windows environment, I just need a card that will allow a tolerable Windows appearance when not running MAME in addition to a great appearance when actually playing.
The only real disadvantage to Windows9x is the 512MB maxium memory limit. The hard drive limitation of 128GB doesn't seem to bother most, but still it does exists. So be aware of it.
Basically, if your willing to run Windows9x, then you will have no problems with AdvvanceMAME or other Windows applications. Contrary to popular practice, you don't have to run AdvanceMAME in pure DOS mode. I don't.