From a hobbyist perspective:
I just picked up a toaster oven with a convection bake mode, no mods at all. The convection bake mode is important, as it more evenly distributes the temperature in the oven which prevents hot spots from frying components or cold spots from forming cold solder joints. I have used older toaster ovens, and they work just fine for hobbyist work, but if you're going to pick up a new one then spend the extra $10 or so to get convection.
I have successfully reflowed many boards with different ICs and have never had an issue. I can't remember the specifics, but I usually give it roughly 90 seconds to come to a "warm-up" temperature, then jack it up to my final baking temperature (I think it spends about a minute or two in that phase). Check your datasheets to make sure your components can handle whatever temperature your solder paste melts at, and for how long. I pretty much eyeball it when I first do a board of a given type to see when different parts reflow based on the amount of solder paste I use, but it's all been pretty similar in my smallish projects.
As far as templates/stencils go, I don't bother unless I have lots of fine-pitched ICs. Get yourself a solder paste kit with a syringe and different tips, and play with those (I used this one from Celeritous: http://www.celeritous.com/estore/index.php?main_page=product_info&products_id=47 there's also a lead-free version). All you need is a sufficient blob of solder paste, surface tension really does 90% of the work if you don't put too much on. I figured out "how much" through trial and error on a few spare boards.
I think if you're not trying to sell stuff and you're not working with sensitive components, no mods are required. In my experience, components are pretty darn robust all things considered, and nothing beats the learning process of watching solder paste reflow on some old boards (and SMT components, if you have some to spare). You'll know when you really need to address the issues you brought up.