In my travels across eBay and the like, I'd say, so far:
Breakers
Metal Slug 1, 2 & X
Pulstar
Blazing Star
Fu-un Tag
Ninja Masters
TSS
Shock Troopers 2
Sengoku 3/2001
And, more recently, I saw my first Rage of the Dragons!
I'm also surprised to have not yet seen a conversion/boot of SSVSpecial? Presumably they made that much harder to reproduce or it's rare on both formats (etc)?
No doubt many more will follow as AES price steadily rise out of control, making buying and, just as importantly, selling legitimate AES carts down the road, much more difficult (i.e. Garou, WW7, MMelee, SW3, KOF 03 etc)
Obviously there's a full list of MVS-to-AES conversions, but those should be much more obvious!
EDIT: Just read Wyndcrossers comments. There probably IS a difference between 'outright' boots and conversions, but if something has been created from something else entirely (i.e. an MVS cart) and has repro labels, insert and manual, then it's pretty much a bootleg imo.
As such, I'm sure all the titles I listed range from conversions to outright boots!