I've got an L4400, gear drive, and it is simply a great basic tractor with superb HP for its size and price. I have 250 acres of woods, roads and a few small fields. I have done moderate land clearing with great success. The strength of the L4400 is that you get a lot of hp in a small, light package for a small price. Its primary weakness is its three point lift capacity is modest and this could limit your choices of medium or heavy duty implements like rotary cutters. It has never been a problem for me.
I don't know much about the 3240. With the GLs you get more nice features like better seat, dash, etc etc. You will also get 3 pt capacity that may be as much or more than the 4400. But you also get considerably less HP.
The M5040 seems like a great tractor to me. It is a true utility tractor and not a CUT. It will handle cat 1 and 2 implements. It is bigger and heavier than the other two and likewise more powerful in terms of hydraulic lift capacity in the loader and 3 pt. It has more, but not lots more, hp than the 4400. It has four drawbacks (to me), the first of which is price, but its not way more expensive than the 4400 or 3240 so that's a tiny issue. The second is weight. If you have a typical standard duty truck you will be pushing or exceeding the limits of its towing capacity with a M5040, loader, loaded tires and an implement. If you have a 250 or 2500 series truck and a big trailer, then that's not an issue at all. The third is implement size. It will take any cat 1 implement but may be too much tractor for light duty class 1 box blades and ground engaging implements. So you either have to be careful of getter bigger, more expensive implements. The fourth is size. The M5040 would not be as easy to use in tight spaces, whereas the 3240 and the 4400 shine in this type of use.
Another potential drawback is no HSt on the M5040. That makes no difference to me and would not want HST anyway.
Having said all that, if I was buying now and had the money, I'd get the 5040. Especially since I don't trailer at all.