Unfortunately, I don't know any program to make music for YM2608. I do know AY-3-8910 though, and there is a lot of program to write music for AY-3-8910 (including ppMCK, VGMCK, XPMCK, Vortex Tracker, and others; eventually FamiTracker will support it too).
It could be added to VGMCK perhaps (the intention is for VGMCK to eventually support all sound chips of VGM format). The program for VGM creators list includes only the emulator "Neko Project 21" as the program that can output VGM using YM2608.
I do know of other Yamaha FM chips and have worked with emulations of them; the VRC7 sound on Famicom is a variation of OPLL (VRC7 has different built-in instruments and has only six channels with no rhythm channels). I have written music for it using ppMCK.
Thanks for the info. I've been on a weird kick trying to find obscure sound chips (at least, obscure for where I live). Speaking of the AY-3-8910, it would be perfect for another thing I'm thinking of doing...I make a lot of modules that only use a square wave sample, to recreate the limitations of making music for an old sound chip. What I was thinking of doing was making recordings of some of my music being played back on an old sound chip. Most of my music would need 4 channels of square wave, but I've got a batch of songs I've been making lately that only use 3 channels, which could be reproduced on an SN76489 (or the clone Sega made for Master System/Game Gear) or AY-3-8910. I was leaning toward just retracking the music on DefleMask and getting a flash cart for my Master System to playback the music, then recording it, but the AY-3-8910 sounds superior in some ways, or so I've read (I don't have anything that uses an AY-3-8910 but I was thinking of getting an MSX..). Anything that uses the AY-3-8910 that could be as easily used as the Master System? Alternatively, if I were to make something that converts impulse tracker modules (ignoring the sample(s)) for playback on Master System, what do you think would be a good starting point (in terms of availability of source code as a starting point for that kind of thing?) I'm thinking converting impulse tracker patterns to a MML wouldn't be too bad would it? Just take s playback engine and make it output text instead of sound...Then we can make stuff in Impulse Tracker supporting programs that plays on video game systems!
I've thought of some more common systems like the Gameboy (not enough square channels), NES (not enough square channels, again) and Sega Genesis (using FM synthesis to make square waves is cheating, but there's a built in SN76489 clone...but it'll sound the same as the Master System).