Some alternative software I tried which also claims to be able to remove silence from MP3s and audio files…

1. mpTrim – (Windows)

Although this software appeared promising at first because of it’s ease of use and batch processing abilities. This package appears to be limited to just three settings for controlling the level silence to remove: accurate (default) (fast), aggressive and very aggresive; none of which were accurate enough for my needs unfortunately.

mpTrim’s blurb…

What exactly can mpTrim do for you?

mpTrim can trim MP3s – removing silent or unwanted parts.
mpTrim can adjust the volume of MP3s. Volume change can be manual or automatic (volume normalization).
mpTrim can fade-in/out MP3s (to fix abrupt beginning/ending).
mpTrim can clean-up MP3s and recover wasted disk space.
mpTrim keeps the music quality intact, no matter how many times you process an MP3, because it works directly in the MP3 format without having to decode/re-encode. That also makes it very fast.

2. dBpoweramp Music Converter (dMC) – (Windows)

dBpoweramp Music Converter seems to need to decode and re-encode the files you want to edit which is too time consuming for my needs. I also didn’t find it very user friendly.

About dBpoweramp Music Converter…

Audio conversion perfected, effortlessly convert to mp3, FLAC, Apple lossless and more. dBpoweramp Music Converter™ has become the standard tool for audio conversions, over 30 million users world trust their converting to dBpoweramp

3. mp3splt – (Linux)

Finally I also tested mp3splt although I was put off by it’s apparent need to split files rather than simply deleting the silence from them. I also have a strong preference for manipulating and editing this kind of file in a graphical environment and I only run Linux as a server.

mp3splt’s description…

mp3splt is a free command-line utility that allows you to split mp3, ogg vorbis and native flac files from several splitpoints, without need of decoding and reencoding. It is useful to split large mp3, ogg vorbis and native flac to make smaller files or to split entire albums to obtain original tracks.

If you are splitting an album you can get splitpoints and filenames automatically from servers on internet like freedb.org, tracktype.org or from a local .XMCD (.CDDB) or .CUE file (see -c option), with the possibility to adjust them automatically with silence detection (see -a option).

You can also try to split files automatically with silence detection (see -s option), trim files using silence detection (see -r option), or by a fixed time length (see -t option)

Or if you have a file created either with Mp3Wrap or AlbumWrap, you can easily split it just with one command (see -w option).