It depends on what I'm carrying....
When I'm carrying Mini Protanks on eGo-style batteries, I have three inexpensive options.
1.
Mint tin lined with craft foam. This is about the size of a box of cigarettes. The clearomizers and batteries travel detached from one another, side-by-side. It looks like this:
That's a 650mAh battery, and not a variable voltage. Not all batteries will fit so neatly in this option.
2.
Hard plastic cigar tube with holes drilled in it. In this case, the clearo is attached to the battery. Holes must be drilled in it, though: airtight is great for cigars, but it will force juice out of a tank.
3.
Hard "clamshell" case for eyeglasses. I got one cheap at the pharmacy. In this case, the clearos may be attached or detached from the battery, depending on the battery length.
When I'm carrying my tube mods, I use something different. I found some clear, 3 ounce, wide-mouth bottles at the pharmacy (on clearance sale) designed for travel use (e.g. shampoo). I took them over to the school supplies aisle to measure and found that they were a perfect height and diameter to hold my mechanical tube mods in 18650 mode (with tank detached). Because they were cheap I bought a lot of them and also use them to carry clearomizer tanks, etc. They fit easily in a pocket or bag.
All of these are inexpensive and adequately protect my gear. As you may have figured out from the shampoo bottle example, it helps to know the dimensions of your equipment so that when you're out and about and happen to see something that might be work, you can measure before buying.