I think it tends to depend on the type of items you're selling, and how buyers usually search for and buy them, plus (perhaps to a lesser extent) the kind of impression you'd like to convey.
As an example, I sell handmade jewellery and craft supplies. I don't really run promotions or markdowns on the handmade stuff, except occasionally I will use markdown manager to discount prices, and I opt for that because it's a clearance price, which I want displayed in all areas of eBay (in search results, in people's watch lists, etc), and I just want the items gone by any means necessary, rather than trying to encourage multiple purchases.
I have some hand-assembled jewellery as well (which refers to stuff where there's no design or real labour involved, I've just cut some chain and paired it with a pendant or something), and I recently experimented with both a promotion (buy one get one free) and a markdown (50% off) on some of those - the markdown was more successful by far, as I had 0 takers for the BOGOF, but several for the 50% off.
The craft supplies are fairly low margin, so I never really used markdown manager for those except on the odd product here and there, again trying for clearance. But I've used the promotions manager very successfully a number of times. People tend to like buying a range of craft supplies, so I opted for the X% off when $X amount or more is spent on qualifying items, and the $X amount was just a little above the average spend from most people who purchase numerous items, so it was kind of meant to be a little cherry on top for people who were already going to be spending money, rather than ecouraging them to spend money in the first place (or in other words, just IMHO, markdown manager is more likely to get people to look, since it will probably be more appealing in search results, while promotions manager is more likely to get people to buy if they're already interested and looking).
So, if people tend to buy more than one of your items, I'd go for one of the bonus promotions, even the accessory discount if people like to buy different, but matching, items (i.e. buy a specific item, get another specific item at a discounted price).
That being said, I tend to use them both quite sparingly (it was a couple of months in between the last two, and mostly because of eBay's promotional credit for FVFs) - I think discounting prices too often tends to mean people will wait until your next promo, or it can give the impression your original prices are over-inflated to accomodate consistent discounts so they'll be more reluctant to pay normal asking prices (as an extreme example, I remember quite a few sellers had some stuff I liked, and every single item in their store was continually 50%, which might've been a lure for some people, but I was watching their stuff for a while and never really understood why they just didn't halve their prices instead, and never ended up buying either - I think the gimmick turned me off 
).
