(M)-LA means it has a floating element, which adjusts the corner sharpness when you focus closer. This option is available on the 50, 65 and 140 I believe and it makes a big difference.
ULD is a version of the 50 involving Ultra Low Dispersion glass and also happens to have a floating element. I've not tried a 50 ULD but have seen some excellent photos from one; in contrast the non-ULD 50 is truly bad: I owned one for a couple of weeks and quickly sold it because it produced notably softer photos than I could get from my 35mm system. If you want to focus closer than 5-10m, I definitely recommend getting the M-LA (and ULD) version of any relevant lens, otherwise why are you bothering to use such big pieces of film?
W I believe means there are half-stop markings on the aperture scale. -N means it has been re-designed; for example there's a 180/4.5, 180/4.5 W and 180/4.5 W-N. The first two are the same except aperture markings, the third is a completely different design (older is Heliar, W-N is Tessar or so I'm told). Since the 180 is basically free these days ($100) it makes sense to have one but I find it a bit short for portraits so will probably get a 250APO soon.
There are APO versions of the longer lenses (210, 250, 350, 500) available that cost $500+ instead of $150.
I would recommend the 110/2.8 over the 90/3.5, just because the 110 is so damn amazing, particularly in the bokeh department. It is a little long for a normal but I use it probably 60% of the time.
There are also SB (short barrel) versions of I think the 75 and 180 which allow use on the shift adapter yet still achieve infinity focus.