I really enjoyed Spiderman 2099 when Peter David wrote for it. He started the series and went through around 30 issues (maybe more). I have that series' entire run (I think it's like 45-50 issues) and I was sad to see it cancelled in the late 90s. The 2099 universe was really cool, but it expanded too much and eventually imploded. Marvel cancelled all of the them, compiled them into one series called 2099 that only lasted like 8 issues. It was nearly unreadable.

Still, the Spiderman 2099 character was great and was easily the best thing to come out of that time period, though Doom 2099 was great as well.

If you can get all the 2099s (and they should be fairly cheap, I think all are only worth their face value) then that would be a good start. But realize it has virtually nothing to do with the Peter Parker version of Spiderman. There are a lot of great callbacks to the 'regular' Marvel Universe, with updated version of old foes as well as some good new ones, so it's better if you're at least familiar with the basic history of Spiderman.

There's also a huge guide to Spiderman. I think it's called "The Ultimate Guide to Spiderman" or something. I own it (I'll look up the exact title when I get home) and it's great because it goes through the entire history of Spiderman, decade by decade.