Desktop Advice

There's a few things to look at and possibly change:

NVIDIA drivers work better in Linux than their ATI counterpart right now. However, the onboard ATI card is not going to allow you to play complex games in Windows, but might be good for a HTPC (especially if you have HDMI out on the board and a TV with HDMI). ATI drivers are decent if you want to brute force your way through some of the more graphically intense games, but lacking in the OpenGL support that NVIDIA has.

You have plenty of hard drive space on Desktop 2 for a HTPC, so that might be your best option to take that one the Linux route. You may want to consider taking one of the 250 GB hard drives out of Desktop #1 and using that as your primary Linux HD (so you can format easily if you need to) with the 1TB hard drive as storage.

XBMC is an amazing application for a HTPC if you have a lot of videos and when properly setup with an Android Phone you don't even have to get up to start shows. The GUI has been changed, but a lot of the instructions of my XBMC Tutorial are still the same (such as setting it up in Mint).

Anyway, barring a new video card in Desktop #2, I would probably use it as your Linux Mint machine and Desktop 1 as your Windows / Gaming rig. I've trying playing games with my onboard HD4290 (slightly faster than yours) and it can do games like Civilization 5 on low settings, but it struggles compared to a dedicated card. It was only really useful while I was RMA'ing a broken card for gaming.

I'm gonna say it depends which one (gaming or development) you want to be vastly better at. Personally, supposing I have Virtualization Technology CPU features available to me, I'd upgrade the phenom machine and just do all android development in a virtual machine. I have an i7 with 6gb of ddr3-1333. I use windows for most everything and a VM for all android stuff. I used to be the other way around, but I stated taking these classes that just didn't work very well in a windows machine. Once I get some more RAM I'll be able to compile android in my virtual machine while playing intense games. I can do this now, but more RAM would just be nice I have a radeon HD5850 1gb GPU FWIW.

I have a tiny gentoo virtual machine (which I use for building eclair & froyo & other android things at work) that I can move between my laptop and desktop hosts, so at work I compile on an old c2d with 3gb of ram (where a kernel will take about half an hour to build), but then I get home and copy the VM over gbit crossover cable to ym desktop, and bam, its all of a sudden a quad core with 6gb of ram lol (where a kernel compiles in just a few minutes)

I'm a big advocate of virtual machines. they are immensely useful and simplify your life as long as you've got the hardware

Phenom IIs are still pretty good right now, so you could overclock it in the motherboard without too much effort as long as you keep it under 64 degrees celsius (if that applies to the 6 core the same as the 4 core). AMD is about to come out with their next model to retire the Phenoms but right now it still does good. I'm using a Phenom II x4 965 overclocked to 3.8 ghz in Linux Mint with two ATI Radeon HD5850s crossfired. The one thing I'd change about my system if I could do it free of charge is to make a lateral swap to a set of NVIDIA cards.

I'm not positive how true this is, but you're probably going to get more use out of compiling with a 6 core processor than you will gaming from it for the time being (I barely compile). A lot of games seem to be poorly optimized for multicore computers (but that may change with the new generation of games). You could go the virtual machine route or the dual-boot route for both machines, the good thing about a virtual machine (with virtualbox) is that you can take snapshots and undo changes you've made if you're testing code on the system. This is good if you don't want to format every time you're testing something. If you dual-boot both of them you could have two decent good machines for a LAN party.