Here's a few tips I've found for scanning magazines.

No specific order but I put it into two sections.
1.
MAIN TIP: Give yourself time! It takes me over an hour to scan a 10-page article. If you rush it you won't do real good.
2.
Scanner Options: Turn on descreening in the scanner options. This will reduce the moire pattern. (I call it "paper texture effect.")
Scan it at a larger resolution then you think you'll need. You can resize it later. This way you'll get readable text. This I learned by mistake when I had to redo a whole batch.
I generally don't like to do color corrections at the scanner level but that's up to you.
By the way, if the magazine back is just B&W, I find it better to do a greyscale scan.
On my Epson scanner software, there's no option to scan as a PNG. So there I scan to BMP, do all the processing (e.g. resizing and cropping) in IrfanView and then save it as a PNG there.
As well, in the "home mode" there's a preset for magazine. Most times I've found it works. Sometimes I need to muck around a bit with the more advanced settings though.
Also, make sure you scan the pages in order so the image file numbers come out in order and you don't need to rename a bunch. Sounds simple, but I've messed up........
3.
Placing Magazine on Scanner: Get a textbook or coffee-table book or something about that weight (not too heavy) about the same size as the magazine. Place it on top of the magazine and it'll flatten it down better. If you don't have one the right size, I've found it best to try to center it to the edge where the spine is.
Use a box to prop up the other end of the magazine so it don't slide off the scanner. This is assuming you haven't debinded it.
If you have bleedthrough issues put a piece of black construction paper between the pages. This depends on the magazine though. Some have nice thick paper while others use newsprinty stuff. If you're not sure test it out.
Here's a tip beforehand if you're not debinding: Open the magazine. Place it cover-up on a surface. Press as hard on the spine as you can. I've never damaged a magazine doing this but be careful. It'll make it more flexible for scanning.
If the magazine is larger than the flatbed it can be tricky. Though I've not done it with magazines, only newspapers, try scanning it in overlapping sections (the more overlap the better) and then stitching it with Microsoft ICE.
Also if you're working with older, delicate stuff (I've scanned a few old books) recommend getting latex gloves so that skin oil doesn't damage it further. (Unfortunately, I'd run out of gloves, which was a bit of a problem
recently......)
One last thing: Before putting the magazine onto the flatbed, check for smudges and dust. I recommend buying a microfiber cloth (I got some at a dollar store). If that doesn't work itself, a tiny amount of Windex might work (spray a small amount on the cloth, not directly onto surface, and I don't think there'll be any problems).
EDIT (2011/10/24): If you are planning to share the scans and there is an address label on the cover (either your own or someone elses') it would be wise to black it out when you edit the scans.
By the way, here's a nice site I found. It's actually for scanning old video game magazines but it can work for others too:
http://www.retromags.com/pages/Guides/scanning