Is there any fix to get rid of this? I know game autosaves on transitions but it's PITA to restart the game all the time.

Also I'm getting appcrash report when I close the game properly.

Did you mean crash after you exit certain area? Did you install Bigg's Widescreen mod in the middle of a play through?

If so..
From an info that i've read (can't find the link, it was over than a year ago), actually it's recommended to start a fresh play through after installing this mod. Those crash during transition is the side effect if you didn't do that. Doesn't matter if you uninstall the mod, the bug will still present. Luckily the autosave function is present.

EDIT: Found the link, it's in this forum
http://www.rpgcodex.net/forums/index.php?threads/planescape-torment-woes.29552/

Yes, when exiting/entering areas. I installed Widescreen mod, together with all other mods, but before even starting the game. I didn't change resolution mid-game.

I've also heard of cache issue, not sure if I should try writing script that clears it every 30 seconds or so?

Maybe you could try it. But i don't know whether it will make it worse or better. The bug usually happen after your enter and exit small area. Some people says this bug exist since the retail version.

I'm think this is the same issue as
http://www.gog.com/en/forum/planescape_torment/yvana_art_gallery_crashes/post31
and has been somewhat solved

Well one fixed 1920x1080 .exe keeps asking for CD 2 to play it...
2nd one crashed but after repeatedly provoking game to crash (entering room, leaving it, moving around a bit, going in again). Let's hope it doesn't crash that often anymore...

The cache issues only really apply to 2CD version and GOG I believe is 4CD. It couldn't hurt to clear it out but a continual script is kinda overkill.

Its more likely crash aqrit linked to. Those exe's are not meant for anyone other than person who posted them. Unless your original exe matches up to their original exe, plus resolution is same...you're going to have problems. Thats why I was patching individuals exe's rather that posting a single one.

So I guess I should reinstall the game and send you exe file to fix it?

Correct.

Just fond some free time to do it. Should I patch it with latest version of widescreen mod or just send it without it?

Patch it with latest and then post your exe along with resolution.

Resolution is 1920x1080

This should be it:
http://www.sendspace.com/file/r9vwfb

So far, so good. I tried provoking it into crashing, but it didn't.
It did hung on one quicksave, and i thought it was about to crash, but it didn't.
I still get message that torment.exe stopped working after I quit game properly, but that's not an issue.
Thank you very, very much!

You're on win7 or vista? That message will be fixed in next update to fixpack. I posted patch data on SHS forums if you want to apply it with hex editor.