... although avidemux still has issues with H.264 encoding, which is almost certainly what you have once Handbrake has done its magic (and may be what you started with as well, depending on your broadcaster). Cutting H.264 is generally an inexact science because of how the format works: it's never as neat as cutting an MPEG-2 stream, for example (look up I-frames for more information if you want to become that video whiz
![Smile Smile](https://forum.kodi.tv/images/smilies/smile.png)
).
comskip is worth looking at, some people have great success with that - it depends on how obvious the commercial cues are (e.g. on-screen graphics changing, aspect ratio changes, etc.). Be aware that it can't handle variable (versus constant) bitrate files, though, which is the default output of Handbrake.
If you're playing the results in XBMC, you could use Edit Decision Lists instead of cutting the file, which allows for some tuning after the fact since they're just text files you can edit at any time.
And if you're just struggling for space, you could always buy a portable external drive or a bluray burner and avoid the 4.5Gb limit of a DVD.