About gems: Go to Gheed, to trade, and check his "magic" tab. There you'll find gem bags for sale. Each gem of any quality, chip, flawed, normal, flawless, or perfect gem, one at a time in the cube with the corresponding gem bag, will transmute into the bag. If there were two of that quality in the bag, the new gem will cube up with the two that were in the bag and appear as a gem of the next higher quality. A gem bad with 100 perfects in it takes less "save space" on disk than 100 perfect gems, so it's a good deal for keeping the 'save size' down.
Likewise, Lysander sells oil barrels, and alkor sells body parts jars.
In my account I keep one mule with all rumes, plus a set of barrels and jars, and mule all these parts to this mule rather often. This keeps my character files a bit smaller.