'best' = subjective; I can offer you a quad-7970 GHz Ed PC which has a lot of GPU power but you're often going to find quad-CrossFire doesn't really work so some of that $2000 GPU spend will be a waste and you'll need to buy earplugs or make sure you like constant loud background music or game audio to deal with the fan noise.
Specifying your parts = assurances of quality of component and exact management of your requirements (no one from a marketing department has decided to save $3 and make more attractive stickers by dumping 2GB of DDR3 in the mix when actually, for gaming, a 1GB DDR5 graphical RAM pool would be a far better option). You can get online retailers to do assembly but it isn't quite like buying a complete PC (I'm not sure how much warranty stuff they do for you - buying components means you need to be able to diagnose a fault so you can ship off the broken part for a replacement, while Dell will take your who PC and tell you what broke and got replaced - they used to ('90s) come to your house to do it but I have no idea is that is standard any more). iBuyPower seem to be the online retailer I hear about the most as a middle-ground between a Dell (who offer very few meaningful hardware options for your build and no brands so you can ensure you get a quality component and not YumCha) and a component store who don't do the 'PC warranty' thing. iBP offer 3 years warranty for labour but only 1 year for parts (despite the parts you specify for the build often having 3-5 year warranties) by the look of it. You pay to ship the case back to them and they fix it so you don't need to know which part is busted (but you have to ship an entire PC to them, doesn't sound cheap to me). They also seem to charge a very steep premium on their components when you select them (and even have YumCha options that make it look more affordable util you realise you actually need to spend $100 to upgrade to a guaranteed decent PSU).
I started building PCs as a kid so I never really got the 'daunting first build' thing. They really are easy, the right thing only ever fits into the right slot in the right orientation so unless you bring a hammer then you can't mess it up (CPUs are square or rectangular but they have a notch taken out of one corner and even some along the side so not only do you have to turn it the right way to get the corner notch to line up but you know you purchased the right CPU for the mobo because the notches along the side only line up when they're electrically compatible. RAM is the same.) But if you'd rather not then getting a friend to do it is the obvious choice. You can buy boxed but it will cost more and you won't be as free to match what you demand and your budget together (you'll either have to pay more or get less, the less will also be uneven so maybe you'll end up with even more RAM than you actually need buy doubly-less GPU grunt to actually game on for the same money as a custom build). If you're fine on limited warranty then look for online shops that assemble for a small fixed fee, otherwise it's usually a lot better to find a non-chain store (just make sure they're not about to go out of business) locally so your retail support if by someone you can drive to.
As for 'best' in a gaming sense (I don't offer things that cost more but aren't much faster or really expensive gear mainly aimed at non-gamign and so costs twice as much, is 10% faster because it's meant for server computational tasks that games don't require because who would make a game that only ran on $300 PCs?). You want a Z68 or Z77 mobo with an Intel i5-3570K CPU and at least 8GB RAM (two 4GB sticks, CL9 1600MHz or 1833MHz at 1.35V or 1.5V). And the big buy for a 'best' gaming rig is the GPU, this can take anything you can throw at it because you can always have more anti-aliasing or other premium effect (which fall to an almost 100% load on the GPU). A small increase in the precision of that shadow map (so Ezio's face looks good rather than having weird diagonal zigzag shadows over it) can easily double the number of pixels it takes so the last 10% of 'looking almost pre-rendered' is 50% of the extra GPU workload. But there is also basically no point buying the best when the almost best is almost best and significantly cheaper, the flip side of the rule is that you can ease off a bit and lose very little except for a healthy saving. I'm going to say an nVidia GTX670 is what you want to be 'best' for gaming, but it is still rather expensive and so isn't what someone who is concerned about price should buy. Someone who wants to go with AMD (nee ATi) would give the equivalent recommendation for a Radeon HD 7950 (which is actually now a bit cheaper than a 670). Both companies do GPUs a lot cheaper (like half that price) that are still solid gaming options but I thought I'd talk about stuff that approaches the 'best'.
Onto that core you want an SSD, something with a modern SandForce controller or one of the competitors that get different characteristics (SF uses on-the-fly compression to do some clever stuff that pairs well with SSD technology but it isn't the best at writing lots of incompressible data at high speed because of it - so a Samsung SSD will reach noticeably differently to anything using SF but they average out to both being rather fast), so a Samsung 830 256GB would be one option. You also want a big drive for archiving and media files so grab a 2TB 7200rpm drive (or even go for a 5900rpm 'green' model as that's fast enough for streaming and rotating platter HDDs are still too expensive for what you get). DVD of Blu ray writer is your choice, they're all cheap as components but I bet blu ray = significant price bump if you buy prebuilt as they're selling you a 'premium digital entertainment experience'. For a self-build you need a case and PSU, don't go cheap on the PSU and for this recommended build you probably want 750W (but 650W would actually be more than enough, it's just nice to give a healthy headroom to avoid trouble and account for a GPU upgrade in 3 years that need that extra 100W+ of power).
You can spend a lot more than buying those parts, but you can't get a lot more gaming unless you just double up the GPUs or buy a graphics card which has two GPUs next to each other (ding so will also increase the required PSU spec and possibly limit the case for adequate cooling) and that's going from fast into crazy & driver issues on launch day with plenty of games. You can SLI/CrossFire, and to get the absolute highest framerates (or to game with 3 monitors in surround vision) you must, but if you want 1080p or a bit more and every game to be great then buy a single GPU today and save the extra $400 and buy another one in a couple of years. Upgrade more often rather than buying it all at current price per processing power (it only gets cheaper over time, which is why selling off your old GPU and buying a new one works).
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