Actually,, I don't really have a preference. Almost all 1000 controllers were slap-on-the-side, so one that offers a pass-thru is really useful. One of the other users here (Shaf) gave me his A1000 gear, and among it was a controller by Comspec that aledgedly autoboots and supports KS 3.1... I have not gotten a chance to try it yet.
I would love to get a hold of a Phoenix Mobo replacement for the 1000 - this is one of the few ways I know of to get an internal SCSI controller and keep the 1000 looking totaly stock.
For nostalgia, my favorite controller was the PaloMax, which was a homebrew ISA RLL controller interface and driver. It was slow and could never autoboot, but it was all I could afford back then (and it used MFM/RLL drives!)
Realisticly, the easiest thing to get for a 1000 now is a Microbotics Starboard with the SCSI option. I see these somewhat frequently on eBay, and even see some online sellers list them from time to time.