I prefer to keep my boot drive external, so that I can quickly boot using another Mac if my primary Mac fails. I use a USB3 drive dock to connect the drive to my Macs.
I bought a 120GB SSD w/SATA3 (6.0Gbps) interface, capable of pushing >500MB/sec read and 260MB/sec writes, sustained.
USB 3.0 is pretty fast -- spec'ed at 5.0Gbps. I'm thinking that performance over USB 3.0 should be at least in the same ballpark as SATA3 (6.0Gbps). It's about an hour of risky, careful work to install the SSD internally in my Mac Mini, is it worth it?