eVGA has been around for many years. My first eVGA card was a GeForce2 MX AGP about 3-4 years ago. December 93 I bought an eVGA FX5900SE - really fine fast card that was maligned by many but works exceptionally well. December 94 I bought a Leadtek 6600GT PCIe and truly love this card. However, the first card I received was defective r/t overheating. It was RMA'd and the new replacement works great.
Both companies have been around a long time and either would serve you well. eVGA has a better warranty (if that means anything to you - I've never had a card go bad - still have VooDoo Banshees and TNT2 Ultras working great), and Leadtek has by far the better bundle. My 6600GT came with Splinter Cell Pandora Tomorrow, Prince of Persia Sands of Time, and Doom3! Plus included the HDTV dongle like eVGA. eVGA used to have pretty good bundles - my FX5900SE came with Ghost Recon and Call of Duty. But it seems eVGA doesn't bundle games anymore. At least they don't throw in crappy games or demos for filler material.
I would choose either one based first on price; if $$$ is close then go with the better bundle. Paid $193 for my 6600GT in December.
Reference cards are video cards produced by chip manufacturere (Nvidia, ATi, etc) before production versions are released. Refernce cards are never sold to the public. It is meant as a blueprint for card manufacturers (Leadtek, eVGA, Gainward, Albatron, XFX, etc) to follow when building video cards for sale. Most card makers stick very close to the reference design, but some have and do deviate from the reference design by using different board layouts, faster/slower memory, connectors, cooling systems, etc.
The bottom line is that if all 6600GT card makers stick very close to reference design (and they do - haven't seen one really different except that one with dual processors on it) the performance of all cards should be very close (and they are). So make your buying decision based on reviews of each particular card (not reference designs), price, bundle, warranty, whatever.