In my experience, Rev. B Blasters had no issues with 3.3V. There is however a known issue with Rev. C Blasters regarding the order of applying power to the target and USB port (see the respective errata sheet and/or note on page 1-3 in the Blaster datasheet).
Shameless plug: Our EEBlaster (
http://www.entner-electronics.com/tl/index.php/eeblaster.html) has none of this issues...
In my opinion 3.3V can be used for JTAG, however there is a lower margin for overshoots then (this applies to all I/Os but might be especially critical for the JTAG lines which typically go of board, i.e. long lines and may be hot plugged). See also:
http://www.altera.com/literature/hb/cyclone-iv/cyiv-51008.pdf, page 5 (from the center of the page...). I assume that this is the background of the 2.5V recommendation for pin 4 from Altera. So you should ensure that there is no overshooting above 4.1V at the FPGA side, e.g. by series resistors and/or clamping diodes (but JTAG clock quality should also not be degraded too much, of course).
In some of our products we use Cyclone IV with 3.3V JTAG voltage and 100R on each JTAG-line which are working without issues (at least together with our EEBlaster).
Regards,
Thomas
www.entner-electronics.com - Home of EEBlaster (EUR 49,-)