Choice, trust, guidance, customer service/support. Don't limit people to what they can put in their rig. Provide options and recommendations based on the customers need and provide a service to help facilitate those needs. Avoid personal bias; don't disown a brand or company because of personal preference, your next customer may be a die-hard fan. You can provide factual recommendations against the product but don't "nerd-rage" on it. We all have THOSE moments. Hardware, Software, and OS are the equivalent of the holy trinity in the tech world; they start flame/rage wars in the blink of an eye. Care about your customer and what they want, you're building their rig not yours. Follow triple C: Courtesy, Commitment, and Confidence.
A Large inventory of stock from all major manufacturers, supreme build quality and excellent customer service/warranties.
Would also be good if you also offered part sales, so someone can just buy a GPU without the need for an entire tower.
Possibly offer an upgrade service, where you pick up someones old tower and then perform the upgrades requested with the parts they have ordered from you and ship it back to them.
The issue with Custom Pre Builds is that the market is pretty saturated as it is and theres probably not much more you can add to help your business stand out, unless you look into software as well as specific builds, perhaps offering things like linux boxes and home servers/NAS builds.
You could also add a benchmark/comparison page with really broad information, so if someone is unsure on what GPU/CPU is better they can just instantly click a button or two and have the products they are viewing directly compared. (would stop the hassle of having to google each product and finding other comparisons)
One thing ive always wanted to see happen is special offers on pre builds and dont mean price reductions on the whole thing , im thinking of offeres that would appeal to gamers and the like.....say when you have plenty of older stock GPU's do a deal buy 1 GPU and get 20% off another identical one or buy this CPU and get this heatsink half price... combo deals that are relevant to the buyers rather than % discounts on entire units.
I would just echo what wbarnes1989 said so well about the importance of service & support. I bought my last rig from a boutique seller, and overall had a good experience. I know I paid a pretty hefty premium for going this route rather than building myself -- in fact that premium was probably close to double what I could have spent on a DIY (yikes!). And the only reason to spend that much more is that you can completely trust that the custom builder (A) really knows what the hell they are doing (B) gives you complete confidence that they are working to give you what you want, with the highest possible commitment to quality, (C) will support you down the line with excellent warranty, tech support etc.
I think a custom builder has to convince the customer that it's really 'on your side' -- that you're a customer that wants something special (otherwise, just buy a Dell) and doesn't want to feel nickle-and-dimed for things, and be sure you're not getting anything you don't want. Things like 'zero bloatware' policies and the like.
For my next rig, I'll probably finally work up the courage (if I can ever find the time) to build my own, because the custom builder route is expensive, no way around it. But I definitely do think custom builders fill an important niche for customers who know about what makes for a high-quality rig, but may just not have the time or expertise to DIY.