Here's the current order of my gear:
* Guitar - Tuner - Vox Wah - Tube Screamer - Amp
* EQ in effects loop

My question is, should I put the EQ after the Tube Screamer and do away with the two extra cables that my sound has to travel through (between the EQ and amp) or am I better off leaving it in the loop?

EQ placement is basically personal preference basically depending on how you use it.
My Rig
>MIM Fender Stratocaster and SX SJM-62
>various magicial noise boxes
>Peavey Classic 50 212

For the funk:
>Ibanez ATK300
>Acoustic B100
well sometimes the EQ can better attenuate/boost the frequencies that are already through the preamp (i.e. in the loop) whereas sometimes people like to set their tone before any amp stage. i guess it all comes down to how transparent your preamp stage is on your amp. but really, it will do the exact same thing it is doing now if you run it inline. plus you eliminate the tone loss due to the capacitance of the extra cable. i know it sounds hi-fi and picky, but if you could a/b the setups, you'd hear it. trust me.
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