You have some old video files there and honestly I advise against attempting to upscale any of the smaller resolution formats, especially the 3gp, flash, etc etc
If you insist on stitching together an old VOB collection into a single container then ok I understand that, but to recode an already encoded mpeg2 (ie not raw footage) of such low resolution (720p) and bit rate is not recommended, however if you must... you can't do better than use x.264 encoder, today is the standard and most supported resulting H264 video.
low quality video will not thank you for re-encoding which looses quality and brightness in the process. I would leave the resolution alone and standardize the container which is compatible with the intended movie players. MKV and MP4 come to mind as the the commonly used therefore compatible with most modern players you choose to watch the movies with.
join the mp2 files together dumping their VOB container is a good plan, I'd recommend mp4 and/or MKV container (MKV for where you want to keep the dolby digital audio)
x.264 is an awesome video encoder if you're insistent on recoding, or are simply
downgrading resolution for small devices
See wiki for ffmpeg encoding and lossless complications
https://trac.ffmpeg.org/wiki/Encode/H.264See VideoLan for x264 codec
http://www.videolan.org/developers/x264.htmlYou might like Handbrake
https://trac.handbrake.fr/wiki/HandBrakeGuideWe are limited by source files quality and destination players/monitors. You'll need to decide on possible future equipment these videos will be stored on and ultimately played on before deciding on codec's and profiles to use.
MKV container would be the most compatible for your source files including multichannel audio.
however I would go for an mp4 container with H264 video, 30 frames per second (or 60 if compatible with your most modern hardware and players), High Profile level 4.2 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio being the most hardware and player compatible (even the ipad mini)..
Unless you have HD multichannel Audio that you'd like to preserve, i'd go with aac for all your audio (btw aac also has multichannel and high bitrate profiles which you might try)..
I'd re-encode a few movies and try them on all possible playback devices before settling on containers and codecs
Your modern monitor likely up-scales for you but I'd never consider up-scaling during re-encoding, as a rule only downgrade resolution.
good luck