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I looked at that case you linked to and the first two reviews are bad.

One person said that the front of the case isn't grounded and he had ruined three motherboards before realizing this.

The second person said that the risers on the motherboard tray are fixed and that the very same motherboard I'm wanting to buy doesn't have the same pattern as the risers and so it won't attach properly.

I like the case otherwise, thanks for pointing it out. I just don't like the reviews.

As far as the price of the mini goes, if you upgrade the drive to 500GB on the 2.53ghz model, buy a wireless mouse and keyboard, and get AppleCare, the price with academic discount is $1076 before taxes. To do any less would not be comparing them favorably for the Mac as the PC would be more than 500MHz faster and would have double the hard drive space.

Even if you subtract the AppleCare, keyboard, and mouse you are looking at $839 before taxes.

Sure, its a Mac and I love the little guy but I'm not sure I want to pay the price premium to still have so little in the way of features.

I'm talking no Blu-ray, slower processor, smaller hard drive, slower hard drive, no HDMI with audio, no eSATA, and a more difficult to upgrade/work on case.

On the other hand you do get Bluetooth, 802.11b/g/n, and a tiny form factor.

But those just don't outweight the minuses in my opinion.

I still haven't totally made up my mind yet but I'm leaning towards the PC very heavily.

IMO:

Save at least $100 by going AMD, probably closer to $150, and drop in a Radeon 4650 or similar for better video playback. (Even the 9300/9400, which is pretty much the best out there right now, is still beat soundly by a current-generation GPU, even for seemingly simple things like video playback (much of which gets offloaded to the GPU now.)

This advertisement peice raises some good points, with the obvious caveat that it was written by AMD to sell Radeons. You'd presumably get similar benefits from going with a GT220, if you're an nVidia fan, and I'm of the understanding that if you're using the GPU for Folding@Home, the GeForce is quite a bit more capable. (Although the people making that claim were comparing higher-end video cards: I think the Geforce 9800 and a Radeon 4870. So the difference may be less pronounced with the lower-end hardware.)

In any case, budget a little extra for a quieter aftermarket CPU cooler and make sure you get a passively cooled video card if you decide to go that route.