Preamble: This is a reference consisting of links to applications and the basics of creating chiptunes in their native format(s). .mp3, .ogg, or other streaming audio formats will not be discussed in this guide.
First up, probably the most popular:
*.NSF, the Nintendo Entertainment System's emulated sound format. Supported by ChipAmp.
Vital Stats: 2 squarewave channels, 1 triangle wave channel, 1 noise channel, 1 DPCM channel. Various expansion chips exist with various benefits.
There are three decent options for this file format, FamiTracker, MML+MCK [warning: moon language] and eKid's s3m->nsf utility.
Famitracker pros and cons:
+Easy-to-use tracker interface
+dedicated NES instrument editor
+can create multi-song *.nsf files
-Still early in development
-No expansion chips supported [yet!]
MCK pros and cons:
+greatest control over sound
+support for all expansion chips
+you basically write the song in notepad
-you basically write the song in notepad
-it's in bloody Japanese. You'll need to ask RushJet1 or someone else for help because I sure as hell can't figure it out.
s3m->nsf pros and cons:
+write a s3m in modplug tracker, screamtracker, or something else that writes .s3m and probably has a nicer interface than famitracker or actually HAS one unlike MCK.
+comes with NES samples made by mv :3 and you can use them in other programs like Renoise or FruityLoops
+update! Now with VRC6 support. Suck it, Famitracker!
-doesn't have as good control over sound as the other 2 options.
*.SPC, the Super Nintendo Entertainment System's emulated sound format. Supported by Chipamp.
Vital stats: 8 PCM channels [kind of boring isn't it?], 64k of sample memory. SPC files being chiptunes is arguable due to the sounds being 100% sampled but most people consider them chiptunes regardless because of the "oldschool sound."
There is only one option that I know of for *.SPC creation, and that's eKid's XMSNES utility. You'll need Modplug Tracker, FastTracker 2, or another tracker that creates .xm files to be able to do this, but it's not so bad. Here is an example song, "artificial sweetener" by funkyfish & raina.
filetypes to cover in the future: .sid, amiga formats and early PC formats [adlib, etc]