I've purchased a few locomotives from eBay with no issue. I mainly purchase at train shows though. I have purchased one PS2 5V locomotive from LiveAuctioneers and it needs a stacker board as the PS2 board is wonky. Some prices are LiveAuctioneer are way too good to pass up but its always a gamble.
eBay recently has had crazy prices so I try to steer clear of it. Train shows are still the best, I can look and touch it. The last Allentown show I picked up a Z-4000 transformer and WOW! I got it for $385 and it works great. I talked to the seller at length about it and he gave me his name & number incase there was an issue we could work something out. Couldn't really test it out while there (plus it weighs a ton) but it runs flawlessly.
I do try to avoid selling locomotives on eBay, I have read too many horror stories about people returning engines after they have tampered with them and eBay always sides with the buyer so youre left with no cash and a now broken unit. I even had an incident with a buyer but was able to clear it up.
With all the new technology and circuitry, id be afraid to buy used unless I could test it, recently picked up the METCA Entenmann's steam locomotive and tender and man that unit is SWEET (no pun intended) but its packed with so much stuff. If I didnt buy it directly from them, I would probably never buy one.