Your question is extremely broad — everything is slow, nothing in particular? That sounds like it has to do more with your machine and your operating system than anything else. Acrobat and InDesign are very different products and they don't have much in common. For them both to be slower is surprising.
Perhaps you can post some simple benchmarks for what you are trying to do that is slow. The simpler the better. New file, place some text, scroll. Or resize. Or whatever.
I don't know why you think that triple-headed configurations are difficult. We have several and do not do anything out of the ordinary to manage them. But if you think that's the problem, unplug two monitors and see if mitigates your problem.
Do you have CS5 and CS5.5 installed at the same time. Run the same benchmark with a stopwatch in both and see what happens.
Do you have 3rd party InDesign plugins or font management software installed? Try disabling it. Conceivably also your anti-virus software might play a role.
i think both applications share a big part: the displaying engine. i have set up a basic test: opening 5 PDFs (select all in finden, cmd+Enter > Acrobat opens 5 PDFs sequentially) and pressing CMD+Q some seconds after (This will shut down acrobat, closing all opened PDFs right after opening has completed). On my machine this takes 33 seconds with this pdf: http://www.baumarkt-ahrensburg.de/fileadmin/pdf/tipps/Bade-_und_Duschwanne_einbauen.pdf; which is about 29 seconds too long for my taste.
I have not installed any third party software in Acrobat, but was unable to test it with CS50, because a downgrade is not possible without fully de-/installing the whole suite.
I have tested repairing permissions, adding a new admin user, macCleaner, Safe-Reboot (yields even slower performance) with no success.
Opening this PDF and 4 copies (5 in total) with Acrobat Reader X within Parallels on the same machine results in total open/close time of 8sec. Which would be acceptable as well; but only on my mac not within emulation
Additionally i do not have any antivirussoftware nor other background software running...
Any further ideas?
Opening these 5 PDFs on my iMac i5 yields in 7 seconds open/close. So i assume a problem with the configuration of the afforementioned 12-core, right?
Besides tricky* tripple head config i use iOne Display Profiling software, BETA, for lion.
*Tricky in terms of: Firefox does not handle tripple head well (windows not opening, windows opening 1px width), iOne pre-BETA does not handle tripple head no matter what, ....
After deinstalling XRites iOne Profiling Sofware the time has reduced to 11 seconds. I have opened a ticket on why profiling software could slow my computer by factor 3 and am now waiting for the answer.
Case closed - thank you for your great support!
*Tricky in terms of: Firefox does not handle tripple head well (windows not opening, windows opening 1px width)
Well, that's not a configuration issue, it's a firefox bug. If you put the firefox window on the leftmost/downmost screen (oversimplification) that'll probably help a fair bit. This is Mozilla Bug 644733 for which I authored a patch in May and a variant of it was committed in August. It's been in the Mozilla 9 tree (Nightly) since Aug. 21, and allegedly it should appear in the Aurora channel sooner or later.
If i put Firefox on the left-most screen, it a) does not open source code view anymore (dragging it to a different monitor for at least 50% of the window size solves it) and b) download-window is opened 1px width - trying to resize it using rightmost-bottom draggabe zone crashes firefox, .. and on and on. In my eyes, firefox is one of the best browsers, yet not the most stable one...
But anyhow: While Firefox (earlier version) was loaded, it sometimes hijacked Shift/CMD-Keys in Creative Suite 5.0. Closing Firefox resumes functionality (oftenly used when dragging+duplicating items or when dragging items along horizintal/vertical guides). Bottomline is: Firefox is buggy at several places, not only in multiple display scenarios...
If i put Firefox on the left-most screen, it a) does not open source code view anymore (dragging it to a different monitor for at least 50% of the window size solves it) and b) download-window is opened 1px width
Ah, well, it does depend on where you have the menu bar, which defines the zero point. Read the details in the linked bug. Short answer is there's a way to make it work by repositioning hte main ff window, or you can updgrade to the Nightly build that fixes it.