http://www.tomshardware.com/t/build-your-own/http://www.logicalincrements.com/CPU/GPU: NVIDIA has had their own share of embarrassments, it is in no way exclusive to AMD. Also, you may want to check out my latest post in Mars' topic. But the bottom line is, whatever you get is good enough. There really are no bad choices within your budget.
Motherboard: You're going to want a motherboard with latest chipset. If your preference is Intel, then the chipset you're going to want is Z97. The problem is, all major brands have about 20 different models with slightly different feature sets. You're just going to have to do a bit of research trying to find what's the best fit for you.
Memory: We're up to DDR4 yes, but there are no motherboards supporting DDR4 yet, unless you want to waste your money on real expensive motherboards. Intel's Skylake should come later this summer that features DDR3/DDR4 support. Might be a good idea to wait for Skylake. Once you have picked a suitable motherboard, please make sure to look up the QVL (qualified-vendor-list) for supported memory brands and models for the motherboard. By selecting RAM that is in the QVL, you reduce chances of compatibility issues between RAM and motherboard.
Sound: The most important aspect to consider is what is the source of your audio. If all you listen to are mp3's, ogg's or whatever that are not lossless, then there is no much sense in investing into a sound card. On the other hand, if you have high-quality lossless audio in flac or equivalent, then it might make sense to invest into audio equipment. But audio investment does not need to be expensive, as long as you don't make the mistake of investing into internal sound cards, they're mostly useless. Instead you can look into external sound cards, like Asus Xonar U7, or any decent USB-DAC. Bottom line, if you upgrade from onboard audio, go for external DAC.
Storage: SSDs around 512GB capacity have become quite affordable. So you may not even need any internal drives other than a single SSD. For storage, any external drive should suffice. You can even hook them to a local network, accessible from any computer in the local network.
Display: Well, there really are two primary factors to consider here. The first is refresh rate. The newest fad is G-Sync (NVIDIA) and FreeSync (AMD). Although as usual, FreeSync is part of the VESA standard and thus can be supported by NVIDIA as well if they're willing. Whereas G-Sync is once again exclusive to NVIDIA. Monitors supporting either should be available in retail. If you want a monitor best suited for gaming, look for those. If you feel they're too expensive or don't like what's available, the second best are monitors that support 144Hz refresh rate. Although in my experience frames higher than 60 are usually difficult to attain in the latest titles even with the best single-GPU available today, but they're still the second best option for gaming.
Now, if you have other considerations than gaming, then you should consider monitors that have IPS panel. They have far superior image quality over the TN panels typically used in home-grade/gaming monitors. Combining IPS panel with high refresh rate and G-Sync/FreeSync is going to cost. A monitor however is a long-term investment and actually a very important one, it is what you'll be staring at every minute you're in front of your computer. A good quality monitor can make a big difference in eye strain.
All that said, take a look at Asus PG279Q. It is not available quite yet, but should be pretty damn impressive. Price tag on it is $800 though.
PSU: Indeed, watts never tell the truth about how good a PSU actually is. Build quality is extremely important and bad PSUs rated at insane watts can perform worse than good PSUs at half watts. My personal preference is Seasonic, but there are plenty of good brands. And funnily enough many of those brands use rebranded Seasonics. This website specializes in reviewing PSUs:
http://www.jonnyguru.com/Case/Fans: Fan-placement is not rocket science, since there are limited number of fan slots. For decent airflow, just place one fan in front, another in back (or up if that is an option) and you're good to go. If you do not like to clean your case, make sure you get a case that is well sealed with no extra holes and that has washable air filter in front. Another thing to consider is how big fans the case can use, I wouldn't go anything smaller than 12cm because smaller ones tend to be noisy. One more thing to consider is how easily a case lets you access the components, a case where opening side panel is difficult or a case where reaching key components is difficult is a bad case.
Peripherals: Logitech G500 is old, I don't think it is being sold anymore. You might want to consider Logitech G502 and Logitech G710 to get some pleasure into KB+M gaming. You may also want to consider Logitech M570 for general desktop use to reduce wrist strain. I use M570 at home and work, and I never use traditional mice for anything but fast-action gaming.
And last but not least, you should invest into internal components in following order.
1) PSU
2) Motherboard
3) Everything else.
Yes, PSU and motherboard are the two most important components in any PC. Make sure they're of good quality.