OK, I'll take another look at foobar's re-encoding methods. This looks like it builds the output directory structure based on the tags instead of the input structure which is one of the things I didn't want but I'll play with it. I have some cases where I have some old LPs I've captured myself - like some old traditional Christmas music which was my grandfather's - and they all might be by "Various Artists" but I keep them in a unique directory tree for several reasons instead of being lumped in with all of the other "Various Artists" on disc (I know they would be in the library view)
Yes, it builds directories based on tags. One other option would be to select 'Source Track Folder' and remove the artist and album folders from Output Style. Then you would have to use a tool or some commandline magic to cut and paste those mp3s and create an exact folder tree duplicate. Probably not that hard if you know how. For the unique directory tree, you can select all those albums you don't want to put together with Various Artists, and put something else in their Album Artist tag. That'll still put them all into the same artist folder.
Also - how well would this handle tagging album art into the destination files and that sort of thing. Now that I write this, I'm not sure if FLAC tags can store album art in every track. I've usually seen the album art as a standalone JPG in the directory with the FLAC files and most software seems to handle it properly when transcoding or importing. More discovery required I guess. The point is that I guess I want to be sure that I just need to be a fusspot with all of the tags and metadata once on the FLAC side and the transcoding using foobar will preserve everything possible (where it translates from FLAC to ID3 tags of course). I guess LAME would replaygain each track, and then I would just tell foobar to do album replaygain on the entire library using tags to build albums and adjust the tags.
Tags are always carried over when the target file is able to store them. And I would always recommend to keep album art in separate files and to let foobar2000 just work through your music collection, either the FLAC one or the mp3 one later, and have the ReplayGain info written into the tags instead of having the volume level altered during encode, for example. But that's just my personal sense of 'order', since I have various devices that should play my files. But since I don't have any album art, someone else might be able to expand on this better.
The reason I want the library re-encoding to handle as much as possible is that I don't want to touch or tweak the destination files or tags at all if possible beyond telling a tool to apply album replaygain if it didn't at encode time - that is also recursive and hands-off. I might end up with FLAC for home, LAME -V2 for work listening where I have quality DAC and headphone amps, LAME -V4 or -V6 for car use, and who knows what - some lower bitrate AAC for a mini-portable where space is very limited and the DAC/amps suck anyways. If I'm going to the trouble to re-rip all of my music into lossless one of the goals is to build the flexibility to produce new copies of my library with whatever encoding I want for a particular purpose. This encludes re-encoding simply because there's been some kind of huge codec breakthrough. I ripped most of my music back in the 2003 time frame with LAME best practices at the time. LAME is even better now, and I feel somewhat inclined to re-encode just because of that. It would be great if I could just point a tool at FLACs, set my new settings and click "go". I'm sure that desire's not unique to me, of course.
The beauty of having your stuff tagged perfectly is that, in foobar2000's example, it will always produce a perfect directory structure as well. And you can save these encoding settings (and in exactly the same way, copy / move settings) and have everything done with a few mouse clicks. This means though that there is the initial investment of fixing all your tags to follow your desired scheme, and of adjusting these encode / copy / move settings exactly how you want them.
I used to have my whole libary in the mp3 format as well and was always reasonably happy with it. That was until I heard a game soundtrack in Ogg Vorbis and it just sounded incredibly good to me. I checked, and the score was encoded at a measly 64kbps. So yeah.. I don't wanna preach or anything, but while you still have time before the big encoding happens, have a look at the more recent codecs too.