General guidelines / workflow to convert or transfer video "professionally"?

I'm an IT "professional" who sometimes has to deal with small video conversion / video cutting projects, and I'd like to learn "the right way" to do this. Every time I search Google, there's always a disaster for weird, low-maturity trialware, or random forums threads from 3-4 years ago indicating various antiquated method to do it.

The big question is the following: What are the "general" guidelines and tools to transcode video into some efficient (lossless?) intermediary, for editing purposes, for the purpose of eventually re-encoding it after?

It seems to me like even the simplest of formats and tasks are a disaster of endless trial & error, or expertise only known by hardened experts who have a swiss army kife of weird conversion tools that they use, almost as if mounting an attack against the project.

Here are a few cases in point:

• Simple VOB files extracted from DVD footage can't be imported into Adobe Premiere directly.
• Virtualdub is an old software people keep recommending but doesn't seem to support newer formats.
• I don't even know how to tell with certainty which codecs a video has, and weather the image is interlaced or not, and what resolution and codecs I'm dealing with.

Problems:

• Choosing a wrong interlace option which diminishes quality
• Choosing a wrong pixel aspect ratio (stretches the image)
• Choosing a wrong "project type" in Premiere causing footage to require scaling
• Being forced to use some weird program that will have any number of negative effects

What I'm looking for:

• Books or "Real knowledge" on format conversions, recognized tools, etc. that aren't some random forum guides on how to deal with video formats.
• Workflow guidelines on identifying a format going from one format to another without problems as mentioned above.
• Documentation on what programs like Adobe Premiere can and can't do with regards to formats, so that I don't use a wrench as a hammer.

TL;DR

How should you convert or "prepare" a video file to ensure it will be supported by Premiere for editing?

Is premiere a suitable program to handle cropping, encoding, or should other tools be used for this, when making a video montage from a variety of source formats?

What are some good books to read that specifically deal with converting videos that use any number of codecs?

What you are actually looking for is an 'intermediate format'. For audio, this normally means uncompressing it to PCM audio (well, ideally it should mean not compressing it in the first place):

ffmpeg -i input.file -c:a pcm_s16le output.wav

For video... well, it's sometimes possible to use either raw video or a lossless codec like huffyuv, but generally you would use a mathematically-lossy but visually-lossless intermediate codec like DNxHD or Apple Prores. AFAIK Premiere supports both of those, but it's been years since I've used it so I could be remembering wrongly. To convert an arbitrary video file to an AVI with DNxHD video and raw PCM audio:

ffmpeg -i input.file -c:v dnxhd -c:a pcm_s16le intermediate.avi

To use a MOV file with Apple ProRes and raw PCM audio:

ffmpeg -i input.file -c:v prores -c:a pcm_s16le intermediate.mov

EDIT: ...actually, thinking about it I believe that Premiere doesn't require the use of an intermediate codec, it should be able to edit most common formats (including the MPEG2 video used on DVDs). That said, intermediate formats are stll very very useful - they reduce the load on your computer's processing resources, since they use relatively simple algorithms.

Is premiere a suitable program to handle cropping, encoding, or should other tools be used for this, when making a video montage from a variety of source formats?

Premiere is an absolutely fantastic tool for such jobs, you could edit a feature-length movie on it fairly easily. I would rate it up there with FCP.

If you want to do things programmatically (i.e. automate shrinking or cropping videos), then a command-line tool like ffmpeg might be better; but for 'creative' editing, an NLE like Premiere is definitely the way to go.

EDIT2: Since you mentioned interlaced video, you can de-interlace it with ffmpeg using the yadif (yet another de-interlacing filter) video filter. I'm not sure if it's necessary for use with Premiere (it probably isn't), and using this on progressive input will spit out horrible output (so make sure you know it's interlaced video), but for completeness' sake:

ffmpeg -i input.file -filter:v yadif -c:v dnxhd -c:a pcm_s16le intermediate.avi

This will work equally well with ProRes, or indeed any video codec ffmpeg can output.

I don't have a full answer, but I do know that mencoder and ffmpeg are two of the most standard tools out there. When transcoding, you're likely best off using one of those tools to perform the actual transcode.

Both of those tools are command line. GUIs exist for them, and I believe a large number of the available tools on the market actually use one or both of those libraries on the backend.

As for whether a file is interlaced and what codec it's using and such, while both tools should be able to tell you, I load the file up in vlc and check the codec information. It's an easy method which gives a good amount of info.