I think recommendations you get from AVS members will be better than Logitech PC speakers, even their 5.1 setups. The best 2.0 PC speakers I've owned that were specifically made for small desk PC locations were the Creative GigaWorks T40. I used these in a 2nd PC location but used a pair of AR Powered Partner 570's with my main PC on a 30" x 60" desk with 30" monitor. I've had the 570's for 18 years and haven't found anything to match them in the $300 range. The T40's sound like cell phone audio compared to the 570's but, after 18 years, I'm looking at the Emotiva Pro Airmotiv 5's to replace them. Emotiva has three powered monitors, the Airmotiv 4, 5, and 6 with 4.5" / 50w RMS, 5.25" 100w RMS, and 6.5" 210w RMS respectively. I believe the sale prices now are $350, $400, and $580. The 5's have a 7.5" x 8.5" footprint, which is slightly larger than the 570's. Audioengine sells two powered monitors, the a2 and a5 with 2.75" / 30w RMS and 5" / 100w RMS respectively. Retail price for these are $200 and $400. Emotiva uses folded ribbon tweeters vs. silk dome for Audioengine. The a2 is tiny ( 4" x 5.25" footprint ) and the a5+ is about the same size as the Airmotiv 5. The Airmotiv are traditional studio monitors with only RCA and XLR inputs and independent volume controls. You'll need a $4 RadioShack 3.5mm to stereo RCA splitter and a standard stereo RCA cable to connect them to a PC. The Audioengine are a more traditional PC speaker and have a 3.5mm input jack on one speaker. One speaker holds the amp and the other is passive. Speaker wire runs from active to passive monitor.
I just gave you a couple of powered options that should fit ON your desk. There are tons of options if you go non-powered with external amp/DAC and put them on stands/shelves. The Polk Monitor 30 II, 35B, 40 II, or 45B are excellent choices for PC audio. I think they are $200 a pair tops for those. Definitive Technology SM350/450 are good choices as well if you can find them at $200 and $300.
And... A note on speakers being " too big " for a room. My A/V room is 15' x 16' and I'm throwing an honest 2600 watts to 11 speakers not including the two 1800w powered subwoofers running at about 40% of peak. I don't think that is too much for my room, well, maybe a little.
HD-DVD = 94
Blu-Ray = 120 ( 24 Warner red2blu )