This is also what I do. For instance Placebo's Burger Queen has around 8 minutes of silence before another segment starts, it's not that great of a second part so I just stop it at around 6 minutes on iTunes.

On rare occurrences though, I do omit a song, doesn't change the order but if there is a song I cannot stand (example: Dark Side Of the Moon - Great Gig in the Sky) I remove it because I will just end up skipping that song.

With listening to albums on Shuffle though, it's pointless unless it's sometype of Best of or compilation album. But albums are made to be listened in order.

Rarely. The three times I have done it have been for:

The Flaming Lips - The Soft Bulletin: Swapped the first Race For the Prize for the remix, and swapped Buggin' and the Spiderbite song for In Slow Motion (like the UK release, which is superior).

Bjork - Homogenic: Switched the album version of All is Full of Love with the intended version, which is a much better song and better end to the album.

Sufjan Stevens - The Age of Adz: Chopped Impossible Soul off the end, because I just do not have the patience for something I enjoy so little.

None of which fundamentally change the structure of the album.

Impossible Soul is such an under-appreciated song...although I do admit I have trouble focusing while listening to it at times.

Oh, I can't stand it. I think it should've ended at I Want to Be Well.

Yeah, all the time. Because I like to imagine I've made the album and Listen to it afterwards pretending it's my creation.

No.
I feel like I'd like my favorite albums less if they had shittier track listings though, I'm anal about openers and closers. I've always wanted to do this though. (#2)

i'm not really bothered of the order of the tracks

some of my torrents come in wrong order, some are divided into 2 folders, etc

but i usually listen to the whole of the album rather than skipping trax

I never change track listings. In fact I go out of my way to make sure they are in the correct order. Like everyone's saying in this thread I feel the tracks are placed in a certain order for a reason and I like to listen to them in that order.

I've deleted a couple of tracks in the past, thinking I'd improve an album and always ended up regretting it (Hail To The Thief). Lately, I've been really pissing myself off, because I've been accidentally leaving my iPod in shuttle mode so I'm usually half way done listening to new albums before I realize I ****ed up the running order, which by the way, is always preceded by the thought..."mmh, I thought this sounded better the first time."

You can completely rearrange Tool's Lateralus and it flows great from track to track. You may have heard about it already but it sounds great even if it wasn't done on purpose.

But I usually listen to albums all the way through.