It's a mixed bag. I've used eBay to buy and sell mainly, but not totally, watches, and I've also used The Saleroom - http://www.the-saleroom.com/en-gb - which is an online live auction house facility. They have their pros and cons.
Local Auctions
If they're local and you can travel, they can be good. You can inspect the goods before bidding, talk to the auction room staff, and there are no postage costs - just travel costs. Buyer's commission can be high - my local house charges 22% buyer's commission and VAT on the commission itself. Other houses charge anything from 15% upwards.
Online live auctions
With the exception of one or two auction houses which specialise in watches - like Fellows (Birmingham), you get very little description of the goods - far less than the best eBay sellers. So, to be sure, you have to email for a condition report, which might be useful or not. I usually ask, "As far as you can tell, does the watch (1) wind (2) set (3) run?" You pay the same commission as being there, plus - if you use The Saleroom - another 3% of the selling price for the privilege of bidding online, plus the postage and packing costs, which will never be less than around £15. So - modified rapture - but I've picked up some bargains over the years.
eBay
I always look for auction lots - rarely buy-it-now lots, unless there's a "best offer" attached - and I always look for lots with a sound description and good photos, where possible. I avoid auctions with "Private bid" bidding lists, because I don't trust them. I set my filters to (1) UK only (2) hand-wound movements and (3) Time: ending soonest - and sit back and see what I get! The eBay buyer's commission is nil - much better than any auction house - and postage costs for watches are much less, on the whole. As long as you're careful, have some idea of what you're really after, and always remember: Caveat Emptor - Let The Buyer Beware - you can get some bargains. The lovely Oris wristwatch I got recently - working beautifully and looking gorgeous in its new strap - was just £26. That's a snip for a watch of this quality.
Just my 10-penn'orth! I think you have to define what you want in your collection - and then take your time and look carefully.