The commercial greenhouses can grow good-looking plants because they have better control of the conditions plants need to grow - temperature, light, nutrition, water, disease and insect control, etc. My guess is that your most limiting factor with your indoor-grown plants is light. Insufficient light will definitely cause spindly plants.
I don't have any experience with a manure-heated covered hotbed, but my biggest concern would be overheating if the cover was left on during a warm, sunny winter day.
Good luck,
Fred

wish I could help you- I've given up trying to start from seed things like peppers, tomatoes, etc. I just plant them outside as early as possible. Have to wait longer for harvest but at least I don't waste a lot of time and money.

A side note- the commercial plants are often bigger but in my experience they are often also rootbound and have other issues. So maybe there is virtue in transplanting smaller stuff you start yourself.

Fred is right. There are many secrets to growing in greenhouses commercial style, however, you can do this organically and do it at home.

I start my vegetables in February, in a cold frame. The trick: PINCH! Give them lots of light (days are getting longer in Feb), the problem with starting seeds in the straw is that light only gets in the top. I tend to put larger plants into that situation, that I've recently pinched back.
I start my seeds in a plastic cold frame that was given to me. It's made out of traditional greenhouse plastic with the channeling in it. One could EASILY be made, and I might make a few of my own like this. They could even be sat on table tops or risers of some kind if needed to be more easily reached. http://apartmentharvest.files.wordpress.com/2007/11/cold-frame-wooden.jpg

Actually you could totally make this from scrap except for the plastic.

But no matter how you grow, PINCHING is the trick to thick, well branched peppers and tomatoes and basils (and many annuals grown from seed). Pinch back after the 3rd set of leaves, pinch that set off.

What kind of plants are you trying to grow? Tomatoes? If so I agree with Fred that you need light and plenty of it from the time they germinate. Warm temps can also contribute to spindly growth in tomato seedlings.

I saw an episode of 'Georgia Gardener' where Walter visited a Bonnie Plant tomato growing facility. The one thing that struck me as being different than what I do ( other than the obvious, I don't have a greenhouse and state of the irrigation and temperature control ) was that they transplanted 2 times before they sent the plants to market. They have a pretty good FAQ on growing from seed in the 'Growing Tomatoes' forum right here on GW.

And I will have to disagree with GGG about pinching when it comes to indeterminate tomatoes and peppers, I just don't see where the benefit lies.

JIM

I said do not pinch your tomatoes! I was pretty clear on what to pinch.

Transplanting twice is a waste of time and money. I work in a greenhouse on small scale. There are so many ways of planting that save time, energy, and resources with start to single potted transplant. It will be the way of the future, the green industry is often one of the least green industries right now. It needs to catch up!

I'm sorry, I understood this;

*But no matter how you grow, PINCHING is the trick to thick, well branched peppers and tomatoes and basils (and many annuals grown from seed)*

to mean that you favored pinching tomatoes.

JIM

"I said do not pinch your tomatoes! I was pretty clear on what to pinch."

Hmmm, I must have missed something too.