Some of the "unofficial" remotes have issues with the odd thing that they don't do the same as the official ones. For example, the iMon remotes tend not to be able to type into the Media Center search-by-name screen using their numeric keypads.
OTOH, one problem with the MS remotes is that a lot of devices respond to them.
The 360 will be default (but you can tell it to only respond to specific 360 remotes and ignore the Windows ones) and my Dell laptop does as well. If I'm using my laptop in the living room while someone is controlling the HTPC, my laptop often responds as well with Media Center popping up while I'm trying to do things. 
Some unofficial remotes also give you mouse control which can be handy (but you'll probably want a mouse/keyboard handy anyway for doing the odd bit of maintenance; you can use Remote Desktop but it boots the TV off and when you disconnect it leaves the screen locked, so you have to reboot the HTPC after using Remote Desktop, which sucks... could use VNC I guess but VNC sucks even more).
Overall, I'd recommend getting an official remote, just so that everything works.
I'd also recommend avoiding anything to do with iMon. I've had iMon remotes & front-panel VFDs ("LED displays") in two HTPCs so far and they've both had crappy software/drivers, software update processes which flat-out do not work (even when they're not detecting software for the wrong hardware), remotes that don't work properly with everything, and hardware issues. I've had to put tinfoil over my current iMon VFD because even though I've configured Windows to ignore its IR receiver, it has a bug in the actual hardware where it goes completely apes**t if it "sees" IR commands for other devices, with the display showing gibberish until the HTPC is powered off at the wall. (HTF did that slip through QA? They only ever tested it in a room where it was the only device!?) A friend has a different revision of the same VFD and the screen is completely unreadable. Yet for some reason iMon are very popular with OEM case manufacturers, despite being absolute trash.
It's a shame Microsoft doesn't make those Media Center IR keyboards
anymore because they had shortcut keys for all the MCE features like TV
Guide, DVD Menu, My Videos, along with the transport controls (Play,
Pause, Stop, Record) and the channel and volume button...oh, and the
green button.
No IR ones anymore but they make bluetooth ones like that:
http://www.microsoft.com/hardware/mediacenter/mediacenter.mspx
I've got the cheaper of the two and it's a good keyboard for the HTPC. IMO it'd be a terrible keyboard for desktop use (due to the non-standard key layout and the horrendous touch-sensitive function keys which are a neat gimmick until you realise that tactile feedback is a good thing), but for doing the odd thing on the sofa with an HTPC, it's good. It has a built-in mousepad which isn't as good as a laptop mousepad but works well enough. (The mousepad seems quite sensitive to reception so if it feels laggy move the bluetooth USB dongle. I used a little USB extension so that it sits on top of the HTPC case and has an unobstructed line to the keyboard and that improved things greatly.)