Here is the full list of appearances by Spider-Man 2099, in chronological order:
Amazing Spider-Man #365
Spider-Man 2099 #1-46
2099: World of Tomorrow #1-8
2099: Manifest Destiny (one-shot featuring Miguel O'Hara)
Captain Marvel Volume 3 #27-30
Exiles #75-99
Timestorm 2009-2099 #1-4
Superior Spider-Man #17-19, 23, 27-31
http://www.comicvine.com/spider-man-2099/4005-40524/issues-cover/