A lot of people argue that farming isn't necessary with the Supply Depot and Fire Crystal recipes available, and that's totally true. But some of us are weird and enjoy it-- and since Advanced Orbs are worth 5132 crowns and Glowing Crystals 272 crowns (as of this posting), the time to money ratio of farming these rarities is actually pretty positive. If you're still a novice knight and aren't doing FSC runs yet, this will especially benefit you!
So, here's what I figured out: Mission 6-1: Axes of Evil looks to be the best place to grab these things. The first depth is Emerald Axis I, which has 10 boxes, and no mandatory combat. It also has 5 mineral deposits in a safe place right at the exit elevator. The only things slowing you down are switches hidden under breakable blocks, and a small area of retractable spikes. If you have a Nitronome or DBB, the switches become pretty negligible. A single run for me takes about 2:25, which is pretty keen for 10 boxes.
The best tips I have on maximizing your efficiency are in this video. It's got a whole bunch of annotations (so if you can't view annotations for some reason, it won't be very helpful to you.) In particular, the tip in the beginning about specifically farming orbs is handy, I think.
http://www.youtube.com/watch?v=wF4bF3oEVVg
Don't forget: have fun playing SK! If this kind of thing is tedious to you, don't do it. Run with your friends, grab crowns, and buy from the Supply Depot. :3
Is Treasure Vault the best place for rarity, orbs and Sparks?