On a fresh started system, free reports about 1.5G used RAM (8G RAM alltogether, Ubuntu 12.04 with lightdm and plasma desktop, one konsole window started). Having the apps running I use, it still consumes not more than 2G. However, having the system running for a couple of days, more and more of my free RAM disappears -- without showing up in the list of used apps: while smem --pie=name reports less than 20% used (and 80% being available), everything else says differently. free -m for example reports on about day 7:

             total       used       free     shared    buffers     cached
Mem:          7459       7013        446          0        178        997
-/+ buffers/cache:       5836       1623
Swap:         9536        296       9240

(so you can see, it's not the buffers or the cache). Today this finally ended with the system crashing completely: the windows manager being gone, apps "hanging in the air" (frameless) -- and a popup notifying me about "too many open files". Syslog reports:

kernel: [856738.020829] VFS: file-max limit 752838 reached

So I closed those applications I was able to close, and killed X using Ctrl-Alt-backspace. X tried to come up again after that with failsafeX, but was unable to do so as it could no longer detect its configuration. So I switched to a console using Ctrl-Alt-F2, captured all information I could think of (vmstat, free, smem, proc/meminfo, lsof, ps aux), and finally rebooted. X again came up with failsafeX; this time I told it to "recover from my backed-up configuration", then switched to a console and successfully used startx to bring up the graphical environment.

I have no real clue to what is causing this issue -- though it must have to do either with X itself, or with some user processes running on X -- as after killing X, free -m output looked like this:

             total       used       free     shared    buffers     cached
Mem:          7459       2677       4781          0         62        419
-/+ buffers/cache:       2195       5263
Swap:         9536         59       9477

(~3.5GB being freed) -- to compare with the output after a fresh start:

             total       used       free     shared    buffers     cached
Mem:          7459       1483       5975          0         63        730
-/+ buffers/cache:        689       6769
Swap:         9536          0       9536

Two more helpful outputs are provided by memstat -u. Shortly before the crash:

User     Count     Swap      USS      PSS      RSS
mail         1        0      200      207      616
whoopsie     1      764      740      817     2300
colord       1     3200      836      894     2156
root        62    70404   352996   382260   569920
izzy        80   177508  1465416  1519266  1851840

After having X killed:

User     Count     Swap      USS      PSS      RSS
mail         1        0      184      188      356
izzy         1     1400      708      739     1080
whoopsie     1      848      668      826     1772
colord       1     3204      804      888     1728
root        62    54876   131708   149950   267860

And after a restart, back in X:

User     Count     Swap      USS      PSS      RSS
mail         1        0      212      217      628
whoopsie     1        0     1536     1880     5096
colord       1        0     3740     4217     7936
root        54        0   148668   180911   345132
izzy        47        0   370928   437562   915056

Edit: Just added two graphs from my monitoring system. Interesting to see: everytime when there's a "jump" in memory consumption, CPU peaks as well. Just found this right now -- and it reminds me of another indicator pointing to X itself: Often when returning to my machine and unlocking the screen, I found something doing heavvy work on my CPU. Checking with top, it always turned out to be /usr/bin/X :0 -auth /var/run/lightdm/root/:0 -nolisten tcp vt7 -novtswitch -background none.

So after this long explanation, finally my questions:

1. What could be the possible causes?
2. How can I better identify involved processes/applications?
3. What steps could be taken to avoid this behaviour -- short from rebooting the machine all X days?

I was running 8.04 (Hardy) for about 5 years on my old machine, never having experienced the like (always more than 100 days uptime, before rebooting for e.g. kernel updates). This now is a complete new machine with a fresh install of 8.04. In case it matters, some specs:

AMD A4-3400 APU with Radeon(tm) HD Graphics, using the open-source ati/radeon driver (so no fglrx installed), 8GB RAM, WDC WD1002FAEX-0 hdd (1TB), Asus F1A75-V Evo mainboard. Ubuntu 12.04 64-bit with KDE4/Plasma. Apps usually open more or less permanently include Evolution, Firefox, konsole (with Midnight Commander running inside, about 4 tabs), and LibreOffice -- plus occasionally Calibre, Gimp and Moneyplex (banking software I'm already using for almost 20 years now, in a version which did fine on Hardy).