Since I seem to get this asked a lot, here's my list of favorite formats:

Video:

h.264 encoded video in an MKV container, most shows that are available for download using BitTorrent and USENET in HD use this format, in 720p. TV shows that are 1080i are usually transcoded to 720p.

Audio:

Lossless flac is my preferred format, it's a FOSS format which is lossless (duh) and uses compression. An average album encoded in flac is around 300 megs, as opposed to 70-100 for an average album encoded via mp3.

Images:

No idea. I do like transparent PNG's though, since IE6 is too stupid to work with them. (Notice what the cyphen.net logo format is?)

File compression:

I like 7z. RAR's alright.

Don't like:

Any formats that use or can support DRM. WMV's are rubbish. M4P's piss me off. Zip is outdated and crap.