Rammy said:
1) Go for basically any i5. If you want bang/buck, that's 3330/3350P/4430/4440 depending on where in the world you are buying. I'd generally skew towards Haswell these days though, there isn't much of a cost difference, and Haswell gives you more motherboard options (H81 specifically. The Superbudget socket 1155 chipset was H61 and that never got an Ivy Bridge refresh)
2) There isn't much difference between ITX and ATX cases in terms of USB connections. Most budgety ATX cases have two front USB 3.0 ports these days, most ITX cases have the same.
A medium-high end ATX motherboard has around 4 USB3.0 on the rear panel, and 2-4 USB2.0. An similarly specced ITX motherboard has about the same.
The main difference would be in terms of internal USB headers. These are often left unused in ATX cases, but can be used for things like card readers and the like.
Basically, whatever you get you are stuck with for USB ports on ITX, as there are limited expansion options. You can always run a USB hub though.
3) Depends. Most cases will come with an intake and an exhaust fan, often of mid-low quality. While they are sufficient for a basic setup, it's usually worth considering your options as you might be able to decrease both temperatures and noise levels by improving the stock setup.
The Intel stock cooler is fine for a non-overclocking setup, though again you should consider this when looking at cases, as they all have different potential for CPU cooling.
4) Yes/no. The best setup is 2*4Gb as it enables dual channel mode, which does increase performance, though not dramatically. If you want to leave room for expansion, there is no major harm in going with a single 8Gb stick, but if 8Gb is all you will ever need then you are probably better off getting 2*4.
5) Again, it depends, on the case, the motherboard, and what sort of cooler you might want to add.
You don't need a cooler, so you are fine with taller memory, but if you want to give yourself more options then it's usually best to look at ones with lower profile heatsinks.
Some general thoughts-
For your needs, it's likely the Elite 120/130 are far better value for money than a Prodigy, which is a lot bigger (has a footprint similar in size to a mid tower but less convenient proportions)
120/125Gb SSD+1Tb HDD is the popular combo for almost everything as it's basically the sweet spot in value for money. A ~60Gb SSD can be a little small if you actually want to run programs from it, and ~250Gb is probably more "high performance" drive space than most people need. 1Tb HDD is popular because it's not a lot more expensive than 500Gb for double the capacity, you might as well.
You shouldn't need a graphics card as such, but it might be something to look into in the future if you are running demanding 3D applications.
PSU depends a lot on availability/pricing. Don't go too cheap here, it's not a place to cut corners. Any basic 400-450W entry level processor is more than enough power, and will cover you for basic graphics cards too.
For motherboards, the main decider is if you need integrated Wifi.
If you don't, then an entry level ASRock H81M-ITX, MSI H81I or Asus H81I-PLUS might be perfect, though check to see if they have enough connections you need. B85 boards might be an option too.
If you do need Wifi, then things get quite a bit more expensive. You are most likely looking at a Gigabyte GA-H87N-WIFI (there isn't really an Asus equivalent).
Thanks for a quick answer, Rammy.
You just made my day/week with that WiFi-headsup. I totally forgot to take that into account. Oh, the amount of kicking and crying that could have ended up with!
Off-topic. THW has caused a serious productivity drop for me. Cannot stop reading the articles and the forum. I see Rammy giving a lot of good answers around the forum. One question though...
How are you keeping the forum free from general crazy stuff(Utube, FB, Twitter, interwebs in general)? I haven't noticed any of the usual nuttyness here.