I would recommend either NCE or Digitrax personally. I have a Digitrax Zephyr system myself, along with a couple extra components for block detection and controlling my switch machines.
The main reason I chose Digitrax was because I wanted to do computer control and automation. I believe Digitrax is the best choice for this because they have the components to do all aspects of it easily in single units (block detection, switch control, signalling) and their network architecture is fantastic, easily the best I've seen out of all the manufacturers. It's basically an computer LAN (almost exactly) and everything networks together really nice and easily and interfaces with the computer beautifully. Most other systems have more limited polled bus architectures and need a separate command bus and feedback bus (Lenz and NCE included), but with Digitrax it's all in one network.
However, if you don't want to do computer control and you just want to run your trains, this doesn't really make much difference to you. I'm in Toronto, and up here my local train shop pushes NCE because they're in New York and they can get fast service whenever needed and they've had great experience with them. I've also had a chance to use both NCE and Digitrax throttles, and I will admit I like the NCE ones just a little bit better. They have nice, plain English labels on the common buttons (lights, horn, whistle, etc) and I like the thumb wheel for speed control, but both of them are very easy to use. Of course, since I use my computer to control everything, that basically becomes my throttle so I don't even need separate throttles for my system personally.
If Digitrax isn't on your list, I'd recommend NCE in that case. I haven't really had any experience with Lenz or MRC, but either NCE or Digitrax would definitely suite your needs fine. If it's a relatively small layout, you'll probably be fine with just the basic starter set from either company. You can run 5-7 trains or so before you'll need additional power.