Does using a lower HT multiplier in combination with a higher reference clock result in higher performance.

Example:
Default - 200x5 = 1000MHz

250x4=1000
or
333x3=~1000

Would the second or third combination give better performance even though they are the same frequency?

Nope.

From what I know, the HTT has so much unused bandwidth that clocking it up won't increase performance, and clocking it down won't hurt you unless you clock it way way down.

Your CPU frequency and your memory frequency should be your main concerns for higher performance. To start overclocking, clock your HTT multiplier down to 4x. When your CPU gets above 2.5 Ghz, kick it down to 3x to keep the HTT from becoming unstable.

Ok, thats kinda what I figured. I already have my 5200+ oc'ed to 3.0GHz and memory at 1000MHz.

Remember the higher FSB more voltage you need to put on your CPU, shorting cpu life so 250 x 4 is better than 333 x 3. Stress CPU dont function well and death one is not reversible.