Yah dremel/jigsaw cuts often look rough, but if you've seen some of the work i've done, I always try to hide the rough edges... For example on my cube case, there are a bunch of holes. The ones on the front bezel have molding around them and swirly fan grills to make them look nice. The ones behind the bezel are not visible so they don't look the greatest. The ones on the top use the fan grills to cover up their edges. The window cut has molding. All the other cuts are not visible.
Now onto windows... there are two ways of doing it. The first way is to cut the window, and then cut the hole the same size, but a little larger. Then get molding and have the window lock into place. The second way is to cut the window shape and to just get a large rectangle of plexi/acrylic and glue it onto the inside of the case. Then you would line the edges with a different kind of molding. Either way works. I bought a kit from
www.pcmods.com .
-Kevin