In the past I have used giftrans without problems. This is
a small public-domain C program which has compiled without
problems on every Unix platform I have used (Sun, IBM R6K, DEC Alpha).
The source, man page and notes can be downloaded from
ftp://ftp.rz.uni-karlsruhe.de/pub/net/www/tools/giftrans/.
Parts of the netpbm utilities can also be used to make
transparent images. Some
notes
are available.