it's all about the id3 tag data.
Using programs such as the Zune software, or something like I use, MediaMoneky, you can completely re-tag your entire collection easily.
Inside the Zune software, start small. One album at a time. If you highlight a single track, right click and select properties, it should tell you in the "TRACK #" field what track number it is. If that field is blank, then the software will default to the next sort-able field, which would be alphabetical.
Going through them all one track at a time, would be cumbersome, to say the least. Highlight the album, and let Zune find the information needed for the album. Then, the id3 tags should be properly filled in with track numbers and all sorts of other information.
But, me being hyper-organized when it comes to my mp3 collection... I start at the folder level.
I make sure that the root folder is the artist, and any sub-folder in the root, is labeled as such... (see picture attached)
And then, my music is named... "<track#:2> <song title>" (the tag of <track#:2> is to have a 2 digit track number at the beginning of the file name... 01 instead of 1)
Each of my mp3's are tagged as such.
If you're looking for a great piece of software to use to do a collection of 100, or 100,000 files, MediaMonkey is what I use, and recommend to ANYONE trying to hyper-organize their collection.
Good luck to you.