You can route the hole for the window in the side panel using a table router or you can pay for someone to cut it on a CNC machine (this is what I did - cost about $40).
Anyway, I used the table router method for cutting a hole in my top panel for a rad and rad grille, but the same principle can be adopted for a side panel window.
Here is how you do it:
1. Remove the side panel from the case.
2. Draw out the design you want for the window opening on a piece of A3 paper (i.e. the template).
3. Copy the design over to a piece of ply / MDF (which needs to be large enough obviously). Ideally it should be about 5mm thick.
4. Cut out the design in the ply / MDF jig using a jigsaw (stay slightly inside the hole you want to cut). Use a fine file to tidy up the edges. How good your jig is will affect how good the final cuts are to the side panel.
5. Cover the side panel completely in heavy duty masking tape and thick paper to protect the side panel finish from scratches.
6. Drill a couple holes in the side panel. These holes will be the same as the holes you to bolt the acrylic window to the side panel so they must be in the correct position. Essentially the holes stop the jig from moving on the side panel whilst you cut it.
7. Correctly locate the jig on the side panel and screw the jig through the holes you drilled in the panel into another sacrificial ply / MDF on the back side. Therefore, your side panel should be sandwiched between the ply / MDF jig and the sacrificial ply / MDF. Note that if you are using a table router then the jig should be on the top. For a handheld router the jig should be on the bottom (the jig needs to be wherever the ball bearing on the router bit is, because the bearing on the bit follows the edges of the jig).
8. Drill a couple of holes through the jig / side panel / sacrificial panel in the middle of the hole you want to route out.
9. Route the hole using a straight cutting bit with the same diameter ball bearing. You need to set the depth on the router bit so that the ball bearing rides around the inside edges of you jig.
10. Un-screw everything and remove the protective paper and masking tape.
11. Then drill a couple of holes (again the right locations) in the acrylic window (cut to the right size).
12. Bolt the acrylic panel to the side panel; using a couple of nuts and bolts at opposing corners. This will 'locate' the acrylic to the side panel.
13. With the side panel and window temporarily bolted together, drill the rest of the holes.
14. Then bolt it all together and bingo you are done.
Here's a pictorial process of what I did to cut the hole in the top panel so that you understand:
Paper template and piece of 5mm ply for the jig:
http://i429.photobucket.com/al...wilson123/IMG_0819.jpg
Completed ply jig:
http://i429.photobucket.com/al...wilson123/IMG_0831.jpg
The whole lot clamped together:
http://i429.photobucket.com/al...wilson123/IMG_0824.jpg
In addition, a long straight piece of stainless steel was screwed to the main straight cuts on the ply jig as an additional guide for the router.
A photograph after the panel was cut, but whilst it's still in the jig:
http://i429.photobucket.com/al...wilson123/IMG_0827.jpg
The finished article (and this was a reasonably complicated shape to cut):
http://i429.photobucket.com/al...wilson123/IMG_0830.jpg
Note that the cuts are perfect. You would be hard pushed to get a better cut with a jigsaw and metal file. The problem with this method is that it is sightly lengthy and the corners are rounded to the radius of the router bit. You could always file the rounded corners afterward if you want.
btw here's a photograph of my side panel with the window cut out on a CNC machine.
http://i429.photobucket.com/al...wilson123/IMG_0930.jpg
Try and cut these shapes using a drill, jigsaw and metal file
EDIT: Is your side panel steel or aluminium? If its steel then the router may have problems cutting it. It may be okay if its thin enough. Try a test piece first on a scrap of steel of the same thickness as the panel, before you go through the effort of making the jig.