I have a Popcorn Hour A-110 and it works very well for me. I had an Apple TV as well but was frustrated with it's limitations and horrible remote. The PCH A-110 works great with MKV, ISO, MP4, as well as many others however it has its' quirks too. I currently use YAMJ as my interface from my Synology to display my movie library:
http://networkedmediatank.com/showthread.php?tid=9862&pid=73102#pid73102
Let me know if you have any specific questions and I'll try to answer them for you.
I'm just now reading about this unit for the first time. I'm in the middle of converting my 250+ DVD library over to an AppleTV compatible format with Handbrake (already imported my 400+ CD collection into iTunes in both Lossless and 256kbit AAC variations (former for archive and broadcast around the house and latter for iPod and car use via my new JVC USB powered car stereo) along with all my photos and a growing music video collection (200+ so far).
Overall, I've been loving the ability to stream my media wirelessly around the house and using my upgraded old PowerMac as a server (was about to buy two new WD 2TB drives that just came out to hold all my music/movies/photos on one drive plus about an extra terrabyte left for future expansion. I use my iPod Touch to control the system with the "Remote" app and have an extra Airport Express "Airtunes" room as well available (giving me 4 zones of music and 3 possible ones for video).
The only thing bugging me after reading a little about the Popcorn unit is that AppleTV is too format limited (without having to convert everything) without hacking, but even if you do hack the thing, it STILL can't do 1080P or pass a 48kHz DTS signal (44kHz DTS CDs play fine through it, though). The DTS thing isn't a huge deal (although my home theater downstairs is 6.1, so DD EX isn't as nice as true discrete 6-channel, but that amounts to all of about 6 titles in my 250+ library.)
I've been thinking of hacking it anyway and adding boxee, a web browser, etc, but I'd be interested in hearing about what people think are the pitfalls and pluses to the Popcorn unit versus a hacked AppleTV (other than the 1080P thing) or vice versa. What total potential does the ATV have that the Popcorn might not have (without its own hacking?) and what can Popcorn do that a hacked ATV cannot do (other than 1080P and pass DTS)?
Perhaps more importantly to me given my setup, are there any simple ways to do the Popcorn unit with wireless? It appears at a glance to be wired ethernet only, which would be a major PITA to run around the house when 802.11N has been working great for me with ATV. I can rent 720P HD movies on ATV and they're ready to play in less than a minute in most cases. And what about streaming music around the house? I can use Airtunes to stream to multiple rooms and even sync them all together to create one giant whole house party mode. I'm guessing that sort of thing is beyond the scope of the Popcorn player?
How does the interfaces compare overall (including boxee on ATV) and are there hacks for Popcorn as well to do more than what it includes? I plan on reading some more reviews, but it's all still pretty new to me on that end. I just read about Western Digital's new player, but its lack of networking sounds bad to me since I want to stream a central collection of music/movies/photos/videos all around the house, not attach a single hard drive to one player unit in one room only.