I used Basilisk II quite a bit more than ten years ago, as sort of a bridge between a Q650 and my more-modern computers. It's good for fast 68k emulation, and I think that's still true today. It's not great for exact timing of those computers, and many shims have been built around it to get it out of the BeOS world and into a cross platform world. I believe the old Basilisk II GUI to set up startup settings without modifying text files was a PowerPC app written in some old cross platform GUI toolkit, and it might have even been Java based. It's a product of its time, and I think Emaculation has done a great job of patching it to keep it up to date despite its vintage.
The two Mini vMacs are made to faithfully reproduce the timings and the output of a Mac Plus and a Mac II. That's not great for fast compiles, but it's great for reliably reproducing what hardware should do to run some apps that bent the rules to run well on the hardware that was available at the time. I've been really impressed by how easy it is to drag and drop raw image files and Disk Copy 4.2 images and have them treated instantly like (at times, really high capacity) ejectable disks.
My preference, and it's probably no surprise given what I've said, is to use Mini vMac II as the emulator of choice. I have a lot of real hardware to handle the oomph of a 68040, a G3, a G4e, and other bits, and soon I'm going to have a POWER9 because I love playing with oddball hardware and getting software to run on it, even if it's incredibly expensive and not practical for the every-person. Putting that out there, it's so nice to have a classic Mac environment, System 6 capable, that's very stable on macOS Mojave. It feels like it's at home with the other apps on the platform and
the Gryphel project that builds and hosts it has great documentation to get it up and running.
That same site has some other cool things like a version of MacPaint built from the source that was donated to the Computer History Museum, with tweaks to allow it to run on later versions of the original Mac OS. Just a lot of fun to experience, all around.