New guy with questions!

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Matt_H gave a pretty good answer, so I'm not adding anything to that, but couple notes:

I actually like the looks of Amiga 4.1 better than morphOS it has a nice retro vibe and feel to it. Also great post and information!

Looks can always be changed Check this out http://library.morph.zone/How_to_Make_MorphOS_Look_Like_OS4

@Iggy I may be going to goodwill today to grab one of those G5 Powermacs to trial morphOS they cost just as much as a mac mini would off ebay.

If you have that kind of opportunity, just go for it! But be sure to get a supported system, more info for example here: http://library.morph.zone/Supported_Computers

Also Is Winuae slower than higher end Amiga 4.1 builds? I would assume it is but by how much?

Depends how beefy PC you have (probably still slower with any PC today), but WinUAE also misses 3D acceleration support (you have to emulate old 2D graphics card under WinUAE). So you are missing gfx speed and also eye-candy features.

[pVC]

Also this mac pro has a quadro in it, all of them did. Which is the best card to slap in these?

Hmmm.. for what use? Mac Pros aren't supported by any amigaish operating system.

I've read the x800 xt is, but That seems awful low to watch videos!

"Low to watch videos", what do you mean? Videos don't exactly require that much from a graphics card... or maybe if you mean hardware decoding capabilities, but none of amigaish systems support those. So in practise it doesn't matter which card you have.. until it supports overlay which makes video scaling fast. So, for G5 machines something like Radeon 9600 is still as fine as the more newer/powerful cards. It's more like if you want 3D stuff run faster with expense of power consumption, then you might consider X800XT etc.

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And I was mostly talking about higher resolution video playback from mplayer and such. I don't think I'll be doing anything using a ton of 3D, but i'd like to upgrade it as much as possible with supported hardware. From the little research I did the x800 xt would be the best, But Just making sure.

Higher resolution playback with MPlayer would be fine with lower spec cards too. MorphOS drivers for lower end cards is pretty fine and movie playback is a lot better than for example with OSX or Linux in the same setup. Most work is done by the CPU, but overlay is pretty optimized on MorphOS. I don't think you'll notice much difference between the supported cards with video playback on a such setup.

http://www.everymac.com/systems/apple/powermac_g5/specs/powermac_g5_dual_2.0.html

How ever I don't think it will work it doesn't seem to have AGP slots. I could be wrong I haven't taken it apart or anything yet.

Yeah that model (11,2) isn't currently supported by MorphOS, support is available for 7,2 and 7,3 models, which are dual processor models, not dual core models.