I love the from scratch aspect.....but, it can be inhibiting some times.
I have fallen into the Joomla trap recently....
when i have someone begging to get a site up, i can put it on a Joomla Template, futz with it and change some css and its done in like no time flat....and it is all manageable by the client (ex client)....
no more headaches, an occassional call but that is it.....
But, as i work on my own sites, it is all by scratch....Its the best way to learn. And like EWebscapes mentioned, it is far easier to ediut a creation of your own than to work within the parameters of anothers creation.
Now, if you were speaking of Templates in some thing like Dreamweaver or something, i would definately say "Use Templates!" don't hack out each page individually. That is a nightmare for upkeep, even if you are using some sever side includes.......
To sum it up, templates are a good thing in different aspects at different times, and if yours are good enough, you could even sell them.