Recently I received prototype boards in which I attached the pull-ups for the TDI and TMS pins to 2.5V like page 10-73 note 6 says is appropriate for my ByteBlaster II. After having problems with the JTAG I started to do more research to find out that the JTAG pins reside in bank1 of the Cyclone III EP3C25F256 which I have tied to 3.3V. To appease the panic setting in, I wanted see in print that the JTAG port could be used at 3.3V with a CIII part. (The fix to make this port 2.5V would require disconnecting BGA pins from the power plane--much easier to connect my pull-ups to 3.3V) I found the following document on the Altera site which says 3.3V is acceptable. Unfortunately as far as I can tell this was missing from the configuration chapter (CH10) in the manual.
Chapter 14, Page 14-14
IEEE 1149.1 (JTAG) Boundary-Scan Testing for Cyclone III Devices
http://www.altera.com/literature/hb/cyc3/cyc3_ciii51014.pdf