There is a lot of data on HIV/AIDS available on the web from different organizations. Unfortunately much of it does not seem to be available as time series.
US Census Bureau -- The US Census Bureau has for many years been collecting data on HIV/AIDS surveys in developing countries. The Bureau provides free access to this data base, The HIV/AIDS Surveillance Data Base at http://www.census.gov/ipc/www/hivaidsd.html . Data can be downloaded in either ASCII or Lotus format.
UNAIDS -- provides a downloadable report on progress in the fight against HIV/AIDS and a downloadable Excel spreadsheets on with country time series data from 1990 to 2009 on HIV/AIDS prevalence, People Living With HIV/AIDS (PLWHA), HIV/AIDS deaths, and other indicators, including for the first time, estimates of HIV incidence. The text version of UNAIDS Report on the global AIDS epicemic 2010 is available in .pdf format at http://www.unaids.org/globalreport/Global_report.htm . The spreadsheet is available under the title HIV estimates with uncertainty bounds 1990-2009 from a link at the bottom of page http://www.unaids.org/en/Dataanalysis/Epidemiology/ .
HIV INCIDENCE -- A time-series of estimates for 1991-2007 of HIV incidence at the country and regional levels is available at http://www.gri.ca/workingp.html