How to remove silence part from mp3 that is extracted from tv drama

You should try something like:

flac -c -d -force-raw-format --endian=little --signed=unsigned input.flac | \
  lame -r --little-endian --unsigned \
       -s 44.1 [other encoding options here] - output.mp3

On the flac side:

• -c means output to stdout
• -d decode
• -force-raw-format --endian=little --signed=unsigned force RAW, little-endian, unsigned output

On the lame side:

• - read from stdin (this is nearly standard)
• -r read RAW pcm data
• --little-endian --unsigned match what lame outputs
• -s frequency: match that parameter with what your flac file contains
• You might need --bitwidth if your flac file isn't 16bits/sample

Concerning the endian-ness and signed-ness, not sure what the "native" format you have is (or how to determine that) - try a few combinations. As long as they match on both sides of the pipe, picking the wrong one should only cost CPU time.

I've used id3v2 before and found it to be quite good.

There are some others according to aptitude: id3 and id3tool. Assuming you have a Debian-based system: aptitude search id3. I'm sure other package managers should have a search facility.

I'm not sure these will be able to do everything you want (by which I mean I don't know anything about Lyrics3 and APE), but you can take a look. Certainly id3v2 has -s, -d and -D flags to remove id3v1 tags, id3v2 tags, and both, respectively (according to its man page).