Can I breed effectively indoors?
Well, if you're thinking you can create farm-quality double crosses, the answer is probably no. It takes selection from hundreds of plants to find the right parents to use. Even without a lot of space for selection, you can do better than making random crosses.
Seedling selection for visual traits will help save space, but this is only useful at the start of breeding. When beginning, start as many seeds from the material to be used as you can so that you have a large enough base to select from. Take at least two clones from each plant, and keep them in the veg stage. Use bonsai methods to keep everything small.
Once you've selected the plants to use for the next generation, discard all of the other clones of the seedlings not chosen. Don't be sentimental, just do it.
Keep good notes, it's easy to get confused, especially when you're high. The down side is that you'll have to be happy with a hundred tiny, seedy plants, instead of big sinsemilla buds. Also if you're not exceeding mandatory minimum sentencing (it's for a good cause, your honor), you're not selecting from enough plants. I know, it's crazy, you might only get a couple grams per plant, with the seeds and all, but its still a hundred plants. Until some one goes to court to set the precedent, I'm assuming 1 plant plus 99 tissue culture vials would be 100 plants, but I don't know. Maybe, you could tell them they are venus flytraps. :)