Some folks use multi-channel analog connections for Bluray if they have a player with better digital-to-analog converters than their receiver/processor. There can sometimes be a problem with the LFE level coming out too quiet, if it isn't getting the required 10 decibel boost, but this is only an issue with certain equipment. Aside from these things, there is no difference from using a digital connection if the audio source is digital to begin with.
All sound produced by speakers is analog in nature: it is a continuous electrical waveform that moves magnets attached to speaker cones. For a digital source it only matters how good the DAC is, where in the equipment chain it is located, and whether any additional processing or decoding is being applied, to determine what the outgoing sound quality will be--the quality of the speakers themselves and the amplification make far more difference.
Most of the really good laserdisc audio that people talk about is digital. Whether the 16/44.1 PCM tracks, the 384 kbps AC3 or the 1.235 mbps DTS, all delivered great-sounding results, and the main reason for this is that they were much more likely to be the original mixes, or versions closely derived from them. Many dvd's and Blurays unfortunately contain remixes, many of which are inferior to the originals, and may well have been made by people who had nothing to do with making the film and have little regard for its proper aural aesthetic. Even a completely lossless encode of an inferior mix cannot compete with a lower quality version of the proper sound.
It's not all doom and gloom though, because there are some releases that still do it right. Apocalypse Now, for example, has always used the original 70mm 5.1 mix, and the Bluray continues this trend (along with a new video transfer timed by a Technicolor reference print, for even greater authenticity). I've never seen the film, but many people like it and will undoubtedly be pleased with the new edition.
