The only difference you will notice from an E6400 opposed to an E6300 at any time is the $40 difference in your wallet.
Maybe at extremely high overclocks such as 500FSB+ you might notice a difference a little becuase of the extra multiplier but the FSB is what's really giving you a lot of your power.
I run an E6300 yes and it's @3.22ghz (460x7)
I notice no difference in gaming or zooming around windows from my stock 1.86ghz. The only difference I even notice is in benchmarks and a little when encoding videos.
The E6400 is not a bad choice like the E6700 is but in my book of Bang for Buck the difference is so small I would put that 40 bucks in a better something else. 40 bucks could be the difference between a 7900GS and an X1950XT. Or even a 7600GT from a 7900GS. This obviously doesn't apply to you since that build has the best vid card but still.
I just look for the best bang for buck and yea sorry i'll send you those links now.
E6300 w/ Arctic Freezer Pro 7 @ 3.6ghz 1.4Vcore
Antec 900 Case
EVGA 750i FTW Mobo
4x1GB of G.skill DDR2-800
2 8800GT in SLI
22" Samsung Syncmaster
1 250GB WD and 1 Seagate 7200.10 in RAID 0
Corsair 520HX 3DMark06 Score: 13900