DVD Flick is nice in many respects, although the menu system leaves a lot to be desired. I especially like the ability to add multiple objects at once and have them automatically parsed to separate tracks with the name of the file as the name of the track. You might take it for granted, but years of using TMPGEnc DVD Author (which has a much nicer, if still simple, menu system) makes that kind of functionality a godsend. For the record, I still use TMPGEnc as my main solution because there are some unique eccentricities to DVD Flick I'm not comfortable with (like only allowing full - and maybe half - D1 when DVD completely allows for CIF/VCD resolution).
My advice - bone up on what makes a DVD compliant, encode all your videos to the MPEG-2/AC3 combo beforehand, and then hand it over to the authoring program. DVD Flick does allow straight copying of MPEG-2 - it's in the main configuration options.
To actually do said encoding, I use:
- AviSynth (filtering/resizing/fps manipulation)
- wavi & aften (to extract the audio and convert to AC3 - the two can be piped together to save HDD space)
- mencoder (to optionally convert the script to HuffYUV-YV12)
- HCenc 0.24 beta (to do the actual encoding to MPEG-2; I have a slew of custom profiles to suit 16:9 and 4:3 video at all three standard framerates and several quality levels)
- DGPulldown (optional; only necessary if the video is 25fps)
- mplex1 or mplex (to do the final muxing of the video and audio into one file; I only use mplex when dealing with the output of DGPulldown, or if I decide to test out 720p/1080p MPEG-2s)
If I have to deal with surround-sound audio, then I also use faad to decode the stream (all of the 5.1 stuff I've encoded came from the Apple Quicktime Trailer site, which only uses AAC), and if necessary, WaveWizard to resample to 48000kHz. aften accepts a standard 5.1 WAV file, and so long as you make sure to use a higher bitrate than the 192kbps you use for stereo AC3 (384kbps or 448kbps are industry norms for 5.1 AC3, although I do mine at 576kbps), it's fine.
To make all of that easier to batch together, yes, it is command-line only. Some of those solutions do have GUIs made for them though. wavi I'm not so sure about, but you can extract the audio from the script with VirtualDub and give it to EncAC3toWAV (which is a frontend for aften). VirtualDub can also be used in place of mencoder since HuffYUV-YV12 can be encoded with ffdshow's VFW interface. HCenc has a GUI (not for the beta, but for main release versions), as does DGPulldown. Unfortunately I don't know of frontends for mplex1 (although it is apparently based on bbmpeg) or mplex, but they're simple enough to use so...