WinRAR shows us that for real-world programs the application performance difference does not reflect the large differences shown in Sandra and RightMark between PC3500 and PC5000. Yes, the differences still exist, but they are no longer quite so overwhelming.
PC3500 at 225MHz is 4.1% slower than PC5000 at 250MHz with tighter timing. Not a huge difference.
On the other hand, PC3500 @ 225MHz is 16.5% faster than at SPD timings, but most of that difference is due to the higher CPU clock speed.
Doom3 is basically scales with the processor frequency and is far more video card bound than anything else (assuming you use the same video card ofcourse - we used the WinFast 6600GT for our tests) and shows very little difference between PC3500 and PC5000 - using the more expensive PC5000 memory only got you a 2% increase in frame rates.
We still do see a noticeable increase between SPD timings and the PC3500 running at 225MHz - 20.5% is nothing to sneeze at - but again, we can attribute most of that increase to the increase in processor clock speed.