I would say you would be better off building a new computer. Here are the reasons:

• Your CPU is probably only good for one more upgrade then it can't go any further. With a new build, you could choose a socket that you could upgrade possibly 2 or 3 more times, depending on how often and what performance you desired
• As you mentioned, your computer uses DDR2 RAM. DDR3 and DDR4 RAM are much faster and will be avaliable for future upgrades.
• A 650W power supply should be sufficient for awhile whether you upgrade or build a newer machine, provided it is of good quality
• Your current build only has a PCIe 1.1 or 2.0 slot. From what I have read (I'm not 100% on this), a PCIe 3.0 card will work in a PCIe 2.0 slot without being slower except for very high end configurations such as the highest end cards or multi-card configurations such as SLI or Crossfire. Still, upgrading would provide you the option of upgrading the graphics several times.

As someone else pointed out, the only parts worth saving are the power supply, optical drive, and hard drive. The case would depend on how easy it would be to put new parts in the case.

My recommendation then would be to build a budget system, picking out the processor/chipset you want to keep and making sure the motherboard is something that will be good for awhile, as that is the component that is the biggest pain to upgrade. However, if you thought just upgrading the graphics card would get you by for awhile, then you could buy that as most cards will probably work in the system. Then you could take the card into a new build down the road when you thought you were ready. Keep in mind that you are more likely to bottleneck somewhere else in this instance, with a modern GPU but much older CPU and RAM.

EDIT: In response to the question update:

Motherboard and processor: You first need to decide on which socket you want to use. There are a couple viable options: LGA 1150, LGA 1151, and LGA 2011. Of these, LGA 2011 is older, but has seen a recent update (LGA 2011-v3, which is not compatible with the older LGA 2011 socket); LGA 1150 is the least advanced but the most available; and LGA 1151 is the newest, but also more expensive. The good news is that virtually any modern Core i5 or i7, and a good amount of Core i3s, that fit these sockets would be faster than a Q6600. As far as future upgrades:

• LGA 1150 will probably see the fewest future upgrades, both to chipsets and faster processors. It uses DDR3 memory exclusively, and also has the fewest USB 3.0 and 3.1 compatible motherboards. However, most motherboards range from $50-200, with a significant portion under $150, and has the most motherboards to choose from (211 on newegg.com, for example).

  • Processors that fit this socket as good as a i7-4790: i7-4790K, i7-5775C, i7-4770K. Note: some high-end i5s, such as the i5-4690K, when overclocked can beat a stock i7-4790 in performance or be so close as to be indistinguishable

• LGA 2011 is a more narrow spectrum of processors, and more high end. Advantages include DDR4 memory, dual full-speed PCIe 3.0x16 lanes on some models, and 6-core processors with large caches. However, many of these advantages are more noticeable in rendering applications rather than gaming, or only in very specific cases. Additionally, most of these processors carry high price tags, and there aren't really entry level processors in this group (the cheapest retails for over $300)

  • Processors that meet your requirements: i7-5960X, 5930K, and 5820K.

• LGA 1151 provides probably the most future upgrades, provides DDR4 memory support, a fairly large selection of motherboards, and much more ubiquitous support for features like USB 3.1. Downsides are that the motherboards are predominately slightly more expensive (more between $150-200), but they do offer more entry-level processors, such as i3 and i5 processors for between $120-220.

  • Processors that meet your requirements: i7-6700K, i7-6700 (limited selection of processors currently, more likely to come).

Graphics: According to this GPU hierarchy, The lowest end card that is an upgrade that is nVIDIA is either a GTX 660 Ti or a GTX 760, but neither are readily available (old). The best value in a low end nVIDIA card is a GTX 950, which will run you about $135-150. An integrated Intel card could provide you with more performance, but it wouldn't be much of an increase over your current card and even the cheapest dedicated GPUs avaliable now would outclass it.

Conclusion

You have two routes that I see as viable both now and longer-term: save a little money now and go with LGA 1150, or go with LGA 1151 and have a longer viable lifespan. Keep in mind that you can still build a really really good machine on LGA 1150 that will still produce impressive gaming results for years, but if you will want the possibility to stay with the latest and greatest, LGA 1151 is probably a safer bet.

Specifics

• Virtually any modern motherboard supports at least 8GB of RAM - indeed, I don't know of any that use either of the chipsets that support less than 16. Basically all of them at least have a single PCIe x16 slot, which is sufficient for basically any graphics card, provided there is physical room in the case and on the board. Also, 6 SATA ports and 6 USB ports (counting connections for a front case header) are virtually standard, as is a 100MBps Ethernet connection. As far as SD slots go, virtually any will support them (usually through a SATA connection), but you'll have to be such a reader separately. With that said, I've picked a board that meets your requirements:

Gigabyte GA-Z170XP-SLI ($129.99). It supports:

• LGA 1151 (Core i7-6700K)

• 64GB Dual Channel DDR4 RAM (4 slots). Can be overclocked up to 3466 MHz.

• Three PCIe x16 slots (supports 3-way Crossfire and 2-way SLI)

• 6 SATA 6Gb/s connectors, 3 SATA Express

• 6x USB ports on the back (mix of 2.0, 3.0, and 3.1). also includes 4 USB headers for the front and a USB Type-C port on the back.

• 10/100/1000Mbps Ethernet

• Front panel audio header (headphone/mic)

Keep in mind I don't have specific experience with any LGA 1151 board - I picked this one because it was fairly well reviewed and met all your requirements at a decent price.