You can usually get mplayer, flash, et al running on 64-bit Linux but it does require more work than a conventional 32-bit quick-and-easy installation. Aside from those initial install/setup routines, the rest of x86_64 Linux should be pretty much smooth sailing.
Quake Wars will not have a native 64-bit client, but using the 32-bit binary with the 32-bit userland will work, just like it works for Quake 4 and Doom 3.
Been running 64-bits Linux since 3 years ago (FC4 through F7) and I can tell you that 64-bits Linux has come a LONG way! It was easy from the start for me to get pretty much everything running, except a few things:
mplayer used to cause major head aches due mainly to the 32-bit Windows libraries for some codecs (with the win32codecs package). It is no longer a problem.
Flash plugin. It has alwasy been a problem. You can either use 32-bit firefox and get rid of many problems, with the overhead it implies (i.e longer startup times, plus more memory) or use nspluginwrapper to install 32-bit plugins in 64-bit firefox. It has the problem that it uses extra CPU cycles and could leak memory like crazy.
Generally, since the data (types) are twice as big, memory utilization is accordingly twice as much, so my personal recommendation for a dual core system in 64-bits is of 4Gb as opposed as 2Gb simply because it would be "the same" as 2GB in 32-bit mode (roughly)
Some apps do take advantage of the extra precision and registers, many others don't, for general use purposes, I still believe 64-bits are "overrated", for scientific work, visualization, multimedia content creation and the like, you DO benefit from the extra mathematical precision and general faster processing of certain data types (like floats and some times (long) integers). For e-mail, office and general browsing, with limited use of multimedia (i.e, consumption and not creation... The benefits are rather slim, though there are).
I've considered going back to 32-bits for some time now, but I always end up keeping on 64-bits... Things are getting easier for stuff such as Java with IcedTea and its preliminary support for a 64-bits native Java Plug-in, hopefully Adobe will soon surprise us all with a 64-bit native Flash Plug-in as well (or so say some rumors, take this with the mount-rushmore of salt grains). All in all 64-bit support in Linux is very mature, elegant and fast.
I tend to keep away from Debian distributions for 64-bits, for the time being, though, as they (for some reason I don't yet have come to fully understand) don't support all that well multilib (coexistence of 32 and 64-bit libraries and binaries, running 32-bit binaries and loading 32-bit dynamic libraries without the need for "jailed" environments [chroots]), and this has lead me to prefer Fedora and SuSE for 64-bit systems, though I tend to prefer Fedora myself. I do believe the problem with Debian and multilib is due to a problem with apt more than anything else, but as I said, I don't fully understand the issue myself.
That 'IcedTea' sounds interesting, maybe someone should package it for Debian. Also ffmpeg should begin to support latest WMA, so no w32codecs are needed. As heavy Java/Flash user with Firefox/Iceweasl 32 bit is much better suited for me.