That's a difficult one to answer Tim, as with all my CS ac the question is, 'What shall I fly today?' and that depends on where I want to fly as I like to keep each airline in its home skies.

For that reason I prefer the 727 as with more liveries it gives me more geographical options. (I've yet to learn how to get repaints). For example today I flew a Northwest 727 from KORD to KMSP just to enjoy some filthy weather, snow at KMSP 

With only five liveries in the base 737 my regions are limited, having said that, I fly mostly around Europe and N America and short to medium hops due to time constraints.

I suppose I fly the 727 more because I've flown on more of them than the 737 and I prefer the look of it, it looks like it means business, it's grubbier than the 737, the cockpit is well worn. My only complaint is the foot warmer does work.

In terms of quality of product there's nothing in it really, along with their 707, 777 and L1011, they all compare.

I find I use the 727 more than any A/c in my hangar. �I love the looks of it and find it much more entertaining than the 732. I feel very at home in it because I've spent so many hrs. with it. �I really like the FE panel in the 727.The pressurization fix works well and it's very �fun to set that up and use it. Plus the Micheal 2 mod and Paul's V-one gauge really bring the 727 to life and enable it to fly by real world numbers. The INS I've installed �works great and adds another dimension as well. �I �didn't know the A/P would never work as it should without installing Acceleration rather than SP2 which I had originally. Thanks so much CS for never bringing that forth in the promo material. Bottom line. With community fixes- very nice. Without- would have been deleted after a month.
The 732- I have problems with rudder input. Sometimes its there, sometimes not. That's the biggest show stopper for me. All the rest of the short comings I've dealt with through available fixes. I just don't use( can't remember what its called) the device that causes CTD. Still missing a functioning pressurization system though. Visually and proportionally the Cs737 is hard to beat and is really beautiful. I'd use it more if it had an update to iron out the most basic problems as has been state over and over and over....... Bottom line here- glad I only paid $12 for it.
So in comparing the two, the 727 gets my vote. Just seems to fly more realistically ( with fixes), from start up to shut down at the gate.