I like Jimbo's idea of building my own system using the best from each package and personalising it myself, but both ClassicWB and AmigaSYS are excellent pre-installed Workbench setups and work fine as they are. If you do end up wanting to build your own system, I recommend partitioning your drive into three or four parts, and make each partition bootable. Install ClassicWB, AmigaSYS, Workbench 3.1 and (optionally) 3.9 on a different partition each, then you can just select which one to boot from and you can mix and match without having to swap any drives.
I think if you want to do the hard work yourself, after installing a fresh 3.1 Workbench these are the next things you should get to start enhancing your Workbench:
Workbench 2000: http://aminet.net/package/util/wb/WorkBench2000
WB2000 update: http://aminet.net/package/util/wb/WB2000_Update