Sometimes programs themselves have a 'benchmark' setting; this is particularly true of the example you give,
Truecrypt. The benchmark can be accessed from Tools > benchmark. The benchmark tests how fast your CPU can crunch through the encryption algorithms (see screenshot). The performance of your machine will be vastly increased if your CPU supports AES hardware encryption/decryption. That setting is available from settings > preferences > performance.
There are specific tests available to gauge GTK+ and filesystem performance in the repositories that can be found with
apt-cache search benchmark, and the benchmarking tool in Peazip will give you some archive compression/decompression figures, which are not particularly useful. That is the problem really, often the results mean little and are what you would expect for your hardware configuration.
Program such as
htop will provide very useful information regarding your current programs and processes, and with
iotop you can see if there is a bottleneck somewhere on your system by studying the data presented. You can study these while performing intense tasks such as encryption/decryption or video transcoding.
phoronix-test-suite, available in the repositories, also has specific tests such as ones for CPU encryption/decryption performance, some for archive compression/decompression, gtk, and for every test you could think of. See my answer in this related question and run
to see all the tests available.