I've now worked on my second show that used footage shot with a Flip MinoHD. There are literally dozens of programs that transcode video, but the best option for converting video to use in an NLE is MPEGStreamClip.
While I've tested this method specifically with Flip footage, it should work for any format that's viewable in Quicktime. If you can't view your video in Quicktime Player, try installing Perian, which enables Quicktime to view a whole slew of different formats.
MPEGStreamClip just works. It isn't bogged down with a lot of iPod presets you don't need, it just opens a video and lets you choose a format to convert to. It offers a few adjustments, but mostly it does one thing and does it well.
I'm an Avid user and will use it for this example, but this workflow should work for Final Cut Pro systems, you'll just want to choose a different compression than I use.
1. Open your video with MPEGStreamClip, and from the menu bar choose File -> Export to Quicktime...

2. In the Compression drop-down menu, select your codec. You should choose a codec based on the format you're finishing in. This project is onlining at 2:1 in standard definition on Avid, so I chose Avid Meridien Compressed. This codec is installed with Avid Media Composer, if you're using a computer without Media Composer you can download the codecs here.

3. Clicking the Options button will give you a few more settings, and I use "RGB Levels (0-255)", "NTSC", and "2:1 Interlaced".
4. Back in the previous window, under Frame Size, select "Other" and type in "720" x "486" for the dimensions. Also, choose "Lower Field First" for the field dominance, despite what the text next to the box says.
5. Uncheck any boxes along the right relating to interlacing, since Flip and most other computer-viewed formats are not interlaced.
6. That's it! Hit "Make Movie" and save the video. The transcoding starts with a progress bar.

7. Once it's time to import into Avid, you'll want to use some specific settings on the "Image" tab of the import settings. Choose "601/709, non-square" because 720×486 is the standard 601 frame size. Choose "601/709" for the Color level, because using the Avid Meridien Compressed codec automatically converts your video to 601 levels. Choose "Even (Lower Field First)" because that's what you chose in MPEGStreamClip. And choose to "Ignore" the Alpha, since there is no alpha channel.
8. Upon pressing OK, your video should import using "Fast Import", since the video is already in the Avid codec. This should save you some time.
And that's it! I've used this method professionally and for small home projects and it's worked every time. Hopefully I can save you some head-scratching.