As mentioned . . . mods really depend on what you want and need.
Honestly . . . I've rarely used or needed a winch. The few times I have needed a winch I had a buddy hook on to me . . . otherwise I usually avoid riding in that type of terrain alone. I do however always have a two strap.
Since I use my ATV for work a plow and boxes -- front and back -- were important. I still need to check the plow fitment to see that it works on the Yamaha, but the boxes I took off my old Honda and stuck on the Yamaha with no issues.
Since I ride with folks most of the time I purchased a mirror . . . well actually a mount. I was able to modify one of my old Skidoo mirrors which I kinda preferred over the look of some of the ATV mirrors I saw for sale (plus I am cheap.)
For me one of the first true mods I will be investing money on will be new tires. OEM tires are usually pretty bad . . . bad in terms of only being two ply . . . and that is the case here. I've got slightly more than 200 miles and already have had three holes, two flats and seven plugs (the good news is that the plugs are holding so my plan is to buy new tires once these wear out . . . assuming the plugs hold.)
But again . . . it really depends on what you are looking for in an ATV. If you plan to mud you want mud tires, maybe a lift kit, winch, possibly even a top mounted radiator. For a person puttering away on a trail they may simply want a new niceties -- a mirror perhaps, seat for a second person, foot rests for the person, etc. For the hunter a gun rack and light bar might be nice . . . (not to spot deer of course -- I'm thinking for coming out of the deep woods after sun down.)