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/