I've used Jiffy Pots in hydro and soil, and I've had nothing but problems with them. Specifically, the 'netting' which provides the Jiffy Pot with its shape does not break down well and may cause your plants to become rootbound before they've even had a chance to take off. I tried cutting the netting off, only to find that the roots were damaged in the process. I've had them fall to pieces in hydro setups which in turn messed my plants up. Also, I've heard from various sources that the peat moss used in Jiffy Pots can harbor dormant pests, though I cannot confirm this from my own personal experience.
After my first bad experience I was buying them at Wal Mart simply because they came with that nice little humidity dome - and they were very cheap, at $1.50 for ten Jiffy Pots and the container - I'd just toss the peat pellets and use the container. However, I've since decided it's even more economical to get nachos at Taco Bell. Eat the nachos, then use the container they came in as a humidity dome for germination and seedlings.