MeGUI is the most comprehensive GUI based ISO MPEG-4 solution. It suports MPEG-4 ASP (xvid), MPEG-4 AVC (x264), AAC, MP2, MP3, Flac, Vorbis, AC3 audio and various common containers support (MP4, MKV, AVI, M2TS).
Here is some bugs with for the current 2013 version of meGUI
a). Under the Options-> settings popup window, under default languages, both drop downs don't list English
b). When converting a 2+ gig AVI file generated from a Nikon S9300 .mov file that is a 2010 frame long HIdef video of 1920x1080 to MP4 it takes 8 hours 30 minutes on an 2ghz AMD compaq laptop with a movie length of only about 30 seconds. It generates an exception log for an unhandled error. See attached. Also when one selects the Queue tab in the program after startup, Job 4 (first on list) shows x264 mode of video, with a status of Error which doesn't show up in the logs. I've downloaded the latest version of x264. This is before I tried to do the one click. The unhandled error is converting directly from AVI to MP4 and not through the intermediary of MKV using one click.
c) My outdoor waterfall video required me to record in the vertical position by rotating the camera 90 degrees. However, there is no way to select a 'rotate' function of any degrees so I don't have to turn my head sideways when converted to mp4. I used other programs to convert .mov to .avi and then used megui after rotation to .mp4.
d). provide setup checkbox option not to check for updates for cases when I'm not connected to the internet. This eliminates those annoying error log messages.
e). and .mp4 to .vob converter.
Please post your bugs there: https://sourceforge.net/p/megui/bugs/
And feature requests: https://sourceforge.net/p/megui/feature-requests/
I will delete our postings here in a few days.
a) already changed in the latest dev build (english is in your build but the list is not sorted alphabetically)
b) please update to the latest dev build and try again
c) not sure about your problem, but you can rotate the video with avisynth: http://avisynth.nl/index.php/TurnLeft
d) already in your build: options\settings\extra configuration\auto update --> disable use auto update