The answer depends on how you're measuring things: by depth of conference from top to bottom, or by strength at the top. As a jumping off point, consider the results from the last four years at the NCAA Championship:
__MEN Appearances Top 15 Top 10 Top 5
SEC 23 13 10 5 __
Pac-10 21 13 10 4
ACC 17 9 6 3
Big 12 15 8 2 2
WOMEN Appearances Top 15 Top 10 Top 5
Pac-10 24 22 13 10
SEC 19 15 11 2
ACC 12 9 4 4
The numbers suggest that on the men's side the SEC and Pac-10 have separated themselves from the rest of the pack. And while each conference has plenty of quality teams at the top end--three of the top five schools in the Golf World/Nike Golf coaches' preseason poll are from the SEC (Alabama, Georgia and Florida) two from the Pac-10 (Stanford and UCLA)--I'd have to go with the observation new Duke coach but lifelong Pac-10 supporter O.D. Vincent made to me this summer: "I think the strength at the top of the Pac-10 is probably as good as it gets, and I think the depth of the SEC is tough to match."
Indeed, schools such as Oregon State and Washington State currently don't contend at the national level while California and Oregon are up and down from year to year. Conversely, Mississippi State is the only SEC school that hasn't made much noise of late. I've got to give the nod, then, to the SEC right now as the toughest men's conference based on the fact as many as 11 teams have legitimate chances to earn bids to regionals.
As for the women, again the SEC and Pac-10 stand out but here the Pac-10's depth is superior. Other than Oregon, the rest of the conference teams (Arizona State, UCLA and USC leading the way) will all have shots at getting bids to regionals. In the SEC, Mississippi struggles, Kentucky looks to be turning a corner but is still a year or two away, and LSU and South Carolina are solid but not always spectacular.
"I feel year in and year out the number of our teams that show up for the national championship and qualify for the national championship is strong," said USC coach Andrea Gaston. "And this past year of course I do consider our finishes [three in the top five] were very strong."
Yes, the Pac-10 also appears to dominate the leader board at nationals, having earned more twice as many top-five finishes since 2004 than the ACC (where Duke has all four) and five times as many as the SEC. And with three of the top five teams in the Golf World/NGCA preseason coaches' poll, it's hard to argue then that the Pac-10 isn't the toughest right now.