Well, if VDubMod doesn't work for you it might be because of your system. It works just fine for me.
If you want to mix in fades, this might be tricky with VDub. I never did or required that though, but I think it has such a option if you have the correct filter enabled. Not sure though.
The thing about appending with only same frame rate and such is good IMO, otherwise it could ruin your movie. Simply reencode the different segment with a lossless codec to the same frame rate and resolution size, then just append it to get the best result.
Mixing sound is not possible with VDub afaik, but for that I just use a Wave Editor through which I have no limits, encode the complete sound in a mp3, and then add it to VDubMod as usual. VDubMod can also handle .ogg and create .mkv or .ogm files without problems.
A video editor will never ruin the movie regardless of the framerates of the input clips. The framerate of the input clips is there only to tell the video editor how to scale the clip, it doesn't affect what the output framerate is. You can have one videoclip at 24fps and another at 30fps and you can output a 25fps mix of them just fine. Naturally the resolution of the clips can be different too. Video editors have advanced algorithms to take care of the details.
Besides, the problems I had were something in the range of about 0.1 milliseconds of difference in framerates. VirtualDub refused to append the second videoclip if it didn't have the exact same framerate, bit by bit. I had to hex-edit the avi to make it the same.
Anyways, we are talking about a completely different class of program. In a video editor you have graphical tracks and you can move clips around with the mouse, you can stretch them with the mouse, you can fade from one clip to another with the mouse, you can mix two videoclips playing simultaneously (eg. with alpha blending or eg. putting one of the videoclips as a smaller image on top of the other videoclip, etc). You can split videoclips, put space in between, add effects, etc etc.
VirtualDub is just a video re-encoder with a few filters.