Well after having both the additional options like running unlinked and the miriad of extra bios options make me really like my 680i that I just installed. The early problems of the 680i have all been fixed, well most that I can see anyways. Early adopters usually have lots of issues that show up alot on enthusiast forums so take all the complaints with a grain of salt. Now the 965 boards run cooler in general so you will really need to keep air moving over NB and SB and some HSF coolers block alot of flow to mosfets so you really want to be careful what you use on a 680i. If you want cheap and fast, get a 965 like the DS3 revision board. If you want to tinker for days and weeks and get an extra bit out of it and have SLI upgrade in the future go 680i.
Now with the R600s coming out you may want to wait to see how they go since they MAY be cheaper and xfire may be the way to go in the near future so dependant on what your gfx card choice is or if you already have a direction you want to go choose wisely now, I would have to regret my choices a week later and have to pay a restocking fee.