I use iTunes (I have a mac) because its easy and it just works. Theres an alternative on Mac and PC called
Songbird so maybe you iTunes-haters could take a look at that.
I often find myself with an audiobook with multiple MP3 files. and for these I use an application called Audiobook builder which converts it to the audiobook format that iTunes recognises as audiobook as opposed to music, so I dont need to make playlists and I dont have files scattered all through my general music collection. Its the only thing that makes sense to me.
Audiobook builder is nothing short of brilliant. and theres a free trial. Theres a free app also, called
Audiobook Binder which does much the same job. I have a/b builder because it was first. Both are also on the Mac app store.
I'm sure there must be PC equivalents, I just havent found a need to find one.
[edit] So I went looking and I found
Chapter and Verse, and
Chapters, both of which look more than adequate to the task