For the NES soundchip, i use Famitracker.
For the sega genesis soundchip, the two best on the net are VGMM (Videogame Music Maker, by Shiru Otaku), and Deflemask, which replicates a whole host of soundchips (NES, Genesis, PC Engine, etc.).
I am far more comfortable with VGMM (sample track). In general most fakebit music sounds, well, fake, overproduced, and usually of low quality (as Tokinsom mentions), and having programs that emulate the real soundchips + expansions are very good indeed.
It took a long time and many lousy tracks to get used to using trackers but I think I've progressed nicely.