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Try running Activity Monitor while you're working, with CPU usage or better CPU history shown in the Dock. If you have Quicktime 7.5 installed, it uses much more cpu in comparison to 7.4.5. A DivX movie played on an Athlon 4000+ needs about 23% with QT 7.4.5 but it needs about 90% with QT 7.5. That heats up the CPU a lot. I always noticed that graphical functions need very much CPU power on the Mac, f.e. the iTunes virtualizer.
Another possible reason are the hardware components and/or the BIOS settings. My Athlon 64 3400+ Socket 754 was also often at 47°C. My Athlon 64 4000+ is with the same cooler, the standard AMD cooler, in normal use at 36°C. My Opteron 185 which has normally 2 x 2.6 GHz runs overclocked to 2,86 GHz on about 38°C with a huge Skythe Mugen cooler. What did you use for heat paste (thermo component)? I always use the Artic Silver 5. Do not apply to much of it. If it's possible, take a look in your BIOS, maybe it has overcloking settings in which you can reduce your CPU voltage. I reduced the core voltage of all my CPUs. Cool'n'Quiet is always activated on my system.
Which hardware components (board, cpu, cooler) and which gfx card do you have? Which image are you using?
2 Opteron systems: OSx86 10.5.8, Andy's 9.8.0 kernel, Asus A8N-SLI Premium, Opteron 185 o'clocked @ 2 x 2,95 GHz (2nd system 2.6 GHz), ATI Radeon HD2600XT 256MB Dual-Monitor 2x HP L2035, 4 GB RAM, Griffin FireWave as main audio device, Marvell + nForce LAN, Asus U3S6 USB3/SATA6 card, 5,5 TB harddisk, Firewire 800 card, Apple Remote + eHome IR receiver, 2x Wacom serial graphics tablet, Canon Pixma iP4700, Logitech Internet Navigator wireless keyboard/mouse combination.
My Audio stuff: M-Audio Transit USB (default audio), M-Audio ProFire 610, M-Audio ProFire Lightbridge (34 channels) using Creamware A16 ADAT converter • MIDI: M-Audio Midiman 4x MIDI interface • Behringer Audio Mixers: Xenyx 1002, Xenyx 1002FX, Xenyx 1202FX, Eurorack UB1002FX, Eurorack MX1804FX, Eurorack MX262A • FX devices: Lexicon MPX100 DSP, Behringer DSP-1000 Virtualizer, Behringer MiniFEX 800 DSP, Behringer Multicom Pro MDX4400 compressor • RETRO: MSSIAH midi/sequencer/synthesizer cardridge for the C64 (Dual-SID), Steinberg M.S.I. MIDI Interface for C64
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