I like FLAC over other codecs, mainly for his size / decodeTime ratio, portability and hardware support. But I think that there are people -like me- that miss the ability to tag individual tracks in a single flac file with cue sheet embedded. IMHO because someone who likes the monolithic idea of having an album in an unique file, also like the possibility of having the tags within the file. So I think that an external database is not the correct solution for this problem (proposed by Josh). Also, someone who is meticulous enought to go lossless, want to tag their files.
Some months ago I started a topic asking for flac further development, mainly because I don't see it as a *complete* software (anyway, IMHO software never is perfect and always can be improved).
Please note, that by "complete" I mean that it lacks some important features. Also, I would like to add that it is the "most complete" lossless codec out there. At least from my point of view.
PS: I think I have read all topic related with this, but maybe I am missing something. If this is the case, my apologies.
Edit: I forget to mention the Matroska container solution, but I think that by using it your are losing the hardware support feature of FLAC