L-jetronic is an old analog EFI, fairly similar to D-jetronic, the main difference is that it uses an air flow meter rather than manifold air pressure and temperature to figure out the amount of intake air. Its electronics are very basic, it uses low-impedence injectors, a simple timing/reference signal, and only later versions actually have an O2 sensor to do closed-loop control. L-jetronic is a fuel-only system. It has a pretty crude warm-up circuit and early versions of L-jet on BMWs have terrible fuel rails (fire hazard) and coolant plumbing.
Motronic is an early digital EFI system (the first car that used it was the E23 7-series in '83or '84). It uses an air flow meter, high-impedence injectors, and a O2 sensor for closed-loop. It can control the ignition system as well, handling spark advance (wasted-spark coil firing) and battery voltage compensated dwell. As a result Motronic is much more efficient for both power and gas mileage. Unlike L-jet, it needs more of a reference signal from the engine (BMW used the flywheel teeth and later a trigger wheel on the front) since it actually controls the ignition coil firing.
As Tony mentioned, the fact that Motronic uses a microprocessor and stores its fuel and spark maps in EPROM allows you to adjust things and tune it (hence the Dinan chips and other products). Early Motronic ECUs have the EPROM soldered to the board so it would need to be unsoldered first, later ones have it in a socket (and those are the ones they have aftermarket chips for normally). Motronic still has a warm-up circuit and thermo-time switches but its version isn't as bad as what is used on L-jet. On BMWs the Motronic fuel rails and plumbing are all done very nicely (in my opinion). Later Motronics (version 1.3) were found on the last M30 cars and they're better than the early versions. Motronic cars don't have traditional distributors as they only need a cap/rotor. This requires, on a BMW, a different upper front timing cover, essentially, and thus the head will appear to be different.
On the E9 side of things, L-jet looks more like D-jet and its manifold clears the brake booster. L-jet uses a traditional distributor. Motronic's manifold looks more like, well, something that had Motronic on it (like an E28) and doesn't clear the stock brake booster. Some people (and La Jolla independent) do Motronic retrofits on L-jet intake manifolds to get Motronic to look more stock and to avoid the brake booster problems, etc.
On a side note, I'm designing an inexpensive 'converter' box that allows you to use a MAF sensor in place of your AFM on your Motronic cars (and maybe later I can make it work with L-jet). MAFs are better than AFMs and they look better as well. We're putting a Motronic engine in my dad's 3.0CS and I'll use that for data logging and testing. 'should be a nice upgrade for the cars with AFMs