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What problems should I be prepared for when using/installing/configuring a system that was functioning flawlessly with 98SE? My hope is that I can still take full advantage of my Audigy2, FX5600, Aopen modem, and the rest of the hardware on my system to allow me to run graphic intensive apps.
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1. "What problems..."
You are already expecting problems -this is good, you won't be let down too harshly then. The biggest problem you will encounter in the
user tasks you have described ("using/installing/configuring") is faulty logic circuits between the keyboard and seat. It ran "flawlessly with 98SE" -great, then there's really no need to use Linux.
There is a considerable learning curve between Windows and Linux. Popular distributions of Linux will install and accomplish
most typical desktop system tasks in much the same way as MS Windows, but the similariaties are only skin deep -the OSs are fundamentally different from the ground up. The transition is like moving from 6th grade to a university freshman in one step -many things are familliar concepts: instructors, students, books, classrooms -but the body of available knowledge is vastly different and far more advanced.
A good suggestion at this point is
www.linux.org they have a free online course that covers Linux basics quite well.
2. "My hope is that I can still take full advantage of my Audigy2, FX5600, Aopen modem, and the rest of the hardware..."
Audigy -works good, not likely "full advantage" though if you define "full" as being special features available through proprietary Windows software.
FX5600 -Nvidia cards are quite well supported in Linux
Aopen modem -likely, even if it's a winmodem. Many people seem to have configuration issues with modems in Linux period. An external serial modem is by far the easiest to configure and will give the best performance for dialup (

to the naysayers) -but a lot of people can't seem to even get them going. Seems that /dev/ttys0 and /dev/ttys1 are just too many choices for a serial port for some people.
the rest of the hardware -yes & no: you are most likely to encounter problems with peripherals like the printer, scanner, digital camera, thirty-button mouse (that you just can't live without), 200-button joystick ...etc.
to run graphic intensive apps -and those would be? not games, please don't say games: A number of 3d accellerated games are available for Linux, but you could run the most popular ones in Windows--maybe only in Windows. Of course you can do photo editing and 3d modeling in Linux using great apps like Gimp (also available for Windows so give it a try) and Povray -but to do more serious animation may require additional (expensive and somewhat difficult to obtain) software -oh yeah, sorry, no Flash/Shockwave creation suite is yet available for Linux AFAIK.
To wrap things up;
Let me just say that I think Linux is fantastic, powerful, and the "cat's meow," but it's definately not Windows. I use Linux almost exclusively but I don't recommend it for everyone. I always like to see another Linux user, so if you are a computer hobbiest, enthusiast, programmer, or IT professional -by all means please give Linux a shot. You won't be dissapointed. But if you are impatient, mainly interested in doing things than really learning computing, then stick with MS Windows or Mac OS.