Cooking overhaul: I really like indepth mechanics in a game, not all foodstuff/drinks you can make have use, but it adds depth and immersion to the game.
Free players on freedom: If it wasnt for this, I probably wouldnt have left GV in 2009 to go to Independence. I still remember the crossing, the huge slopes of dirt, the huge STONE buildings, caravels everywhere, ... it got me hooked and never let me go. The friends I crossed with gave me their referalls so I could be prem and in that time I was able to poke an irl friend to use his paypall for my wurm subscription (and now ended up with paysafecards :p), never skipped a month of prem since
RMT changes: Good and bad I suppose, I'm a bit neutral on this, but it still one of the better changes to wurm. (Discussed it in the topics back when the change was announced, so I wont go repeating it here again to not create a wall of text :p)
Other changes that come to mind (mostly from when I started in 2009):
Bulkbins being introduced! This was a big one for me, I was still playing on GV, so before bsb's were a thing in wurm, I had to chop trees to make 20ql planks whenever I wanted to make another house, some more fences or to repair damages (decay was brutal on GV, but managable if you did a routine repair route every month or 2 ;)). And after they were ingame... I could actually just stock up on every 20ql material I could make, an could bash down the coffins and containers-in-containers-in-containers that I used befor!
Large anvils going down to 10kg instead of 50kg. This was a huge change for me also, since when you failed creating back then, you'd end up a with scrap and could start mining iron all over again. And let me tell you, mining on GV with 20skill, no woa enchants... wasnt really "fun". (that and combined with how long it took for a 20ql forge to actually smelt the ore down to lumps and keep them warm long enough for you to smith with)
Plotting course: A more recent addition, but holy Magranon was it a good one, simply choose the server you want to cross to, and sit back and relax (or zigzag against a gale... x_x)
Archeaology: Simply, another indepth new mechanic added to wurm, that actually got my lazy ass of my deed to go explore, looking for old deeds and fragments.
Permission system was a a great one to, finally I could fine-tune who could do what on my deed and who could pilot/sit in what cart/ship
Changes from the list I didnt pick:
Multistory buildings: Mixed feelings about this one, it led to extreme freedom in creating awesome buildings, but for me, I never end up using all the floors on my buildings XD And its "mixed" because suddenly, the Wurm client ate up 1-1.5gig of ram instead of 150-200Mb of ram... bye bye being logged on with 6 accounts digging and mining (back then a year of prem was 50euros, so I could actually afford allot of alts just for digging/mining)
Graphics overhaul: Altho a welcome change, it wasnt something I really needed, I'm usually not to bothered with the graphics of a game. It had its charms back in 2009, judging if your crops were ready by placing small barrels all over your farmplot, seeing crazy colored animals, standing on horses, etc...