For me it depends on what I'm hooking up to what - generally these days I'm running digital out (via S/PDIF) to a DAC, which is then feeding amplifiers with their own integrated volume controls. In that setup, everything on the computer is set to 100% EXCEPT my surround sound simulacra software (which I only use for videogaming),* which defaults itself to something like 70% (Windows master volume control) - you can over-ride it but you can get a bit of clipping on peaks in some games, which is probably the result of whatever downmix coefficient matrix they're using coupled with the game itself maybe running pretty close to full-scale. Thankfully that volume setting is remembered in its software switch, so this is basically a set-and-forget thing. For music or movie playback its 100% everywhere.
If I'm connecting to the PC's analog outputs into some device with its own preamp, I will usually start at 100% on the PC and then back it down as needed, because sometimes its too hot relative to the device's input sensitivity (and I want more "range" on its volume control).
Software on the PC, like media players, in-game audio master settings, etc is always at 100% and the only control I'll be adjusting on the PC is its master output. I don't know if this is empirically best, but its the most convenient and consistent (e.g. I always know where I'm fiddling with the levels so there's never "man this just isn't getting loud" and then have to remember I may have set some per-application thing previously).
* Razer Surround Pro. It defaults its output to less than 100% in Windows, but it also applies DR compression for the same (this compressor can be defeated). If I had to guess this is because some games probably assume they can go 0 dBfs on every channel (which would probably not be an issue if you had an actual 5.1 setup), and the coefficient matrix that Razer has selected isn't dropping every channel by some fixed level to compensate for that (like -6dB) before calculations, because they want to preserve lower intensity sounds as well. I've not noticed any problems with DVD multi-channel downmix to stereo in whatever player application warranting a slight reduction in the master output, so it does seem to be specifically related to videogames. And yes I've tried it both ways - probably 98% of the time leaving it at 100% there's no noticeable problems (or really any differences), but periodically there's brief signal clipping and it gets annoying, so back to defaults it went, and there's been no issue with signal clipping since.
PS: FWIW I do largely the same thing on my Mac, but its pretty old (its a G4), and I don't know if that's in any way similar to modern OS X audio (I know in the Windows and Linux worlds, lots and lots has changed for their respective audio subsystems over the same time period).