There were two Topps sets per movie, which would be considered the 'standard' sets. Each set had 90 cards plus foils and autos. Each update set (ie the second for the movie) had 90 cards plus foils and memorabilia (costume) cards and some autos. If you look at eBay for LOTR autos, the clean looking white background autos are the ones from these sets.
In addition, there is the Trilogy set - a chrome set. This was less popular and if autos are your thing, the autos tend to be a fair bit cheaper.
Finally, if you are into sketch cards - the relevant sets are Evolution, Masterpieces I and Masterpieces II. There are some amazing sketches but also a lot of duds and boxes can be quite expensive. These sets also had foils and the Evolution series has my favourite chase set - Stained Glass (plastic semi-transparent cards with a stained glass look).
So, my recommendation would be the original 6 movie sets (some boxes still around) for autos/memorabilia, Trilogy for a single set that covers everything, and the last three if you want sketch cards.
Many of the other sets are promotional sets of various kinds. I think I have a couple of different 20 card Cadbury's sets for example. There were also 'Action Flipz', small lenticular cards.