The differences in B-series trannies is the gearing. Most VTEC trannies have more aggressive gearing than the non-VTEC version and also a higher final drive. It's similar to comparing a 10-speed bike. Think of the VTEC gearing as being 1-5 and the non-VTEC gearing being 2-6. You won't accelerate as fast with the 2-6 but the longer gearing means the engine has less work to do to keep you at speed (lower highway rpms for better gas milage and less engine wear).

Which is best? That's subjective to what you want. If you want a good daily driver that gets great gas milage and are willing to loose a little performance, stick with the LS tranny (also, if your cheap, this is best). If your looking for more performance, their's the B18C1 and B16A trannies (the B16A, depending on year and what car it came out of, is usually a little more aggressive). You can sometimes find JDM trannies with a factory LSD and the ITR trannies as well. Seeya.