I keep my PTO shafts on the implements they belong to. I usually wire them up or use bungee cords to keep the end from contacting the ground. I also separate them when I use them for the first time at the start of the year, add a layer of grease. I dont use marine grease or anything, just cheapo standard grease.
For example: I need to get out and till the garden plot soon. I plan, in the coming weeks when I have a few minutes, to hook up to the tiller and bring it up to the 'shop.' I will disconnect the PTO from the tractor (I do not transport the implement without the shaft hooked up) and separate the halves, leaving the implement side on the implement. I clean and inspect the shaft halves. I use calipers to measure the stick-out on the bolts of the slip clutch and loosen them. I rotate, by hand obviously, the PTO and inspect the blades and bearings. Check gear oil and lube everything. Put the halves back together and hook it up to the tractor. Slip the clutch a few times (mark it with a sharpie to ensure the two slip) and retighten to the measurement, check slip again and all should be good. Make any adjustments needed for depth or whatever and it's ready for work.
My implements are stored outside. When I am done with them for the season, I inspect them again, fix anything that needs it. I keep them up on blocks, grease everything, make sure the PTO shafts are not in the mud, and dont worry about it until next spring/summer when they are needed again.