Boxee, a company whose set-top box and media center software bring virtually any Web video content to the television screen, finally launched its iPad app today.

Recreating the experience of the full-size version of Boxee would be impossible on the iPad, given the widespread use of Flash-encoded video on the Web and Apple’s refusal to support it. Instead, the app was thoughtfully designed to make the most of the features that are most appropriate for the iOS platform.

Noticeably absent from the app is any attempt to recreate the “Apps”, “Movies” or “TV Shows” tabs from the TV-friendly version of Boxee. Too much of that content utilizes Flash and converting it all would be well beyond the scope of what an iPad app of this nature should be expected to do. Chalk it up to a limitation of the platform.

Watch Videos From Twitter and Facebook Friends

Boxee’s iPad presence is decidedly social. The “Friends” stream, which pulls video links from your network’s Twitter and Facebook posts, is also a feature on the television-sized version of Boxee, but it’s more front-and-center on the iPad. In a sense, it’s like Flipboard for video, but with more limitations on what content can be displayed.

For example, Wired’s Tim Carmody shared a link on Twitter to the latest episode of the FX comedy “Louie.” It showed up in our feed, but when we tapped through to watch the video, it couldn’t be displayed because it came from Hulu, which utilizes Flash and notoriously blocks Boxee from accessing its content anyway. Attempts to load Hulu videos from the Boxee app result in a prompt encouraging users to subscribe to Hulu Plus and download their app.

The feature works beautifully with YouTube videos, which are displayed natively within the app itself. Other HTML5-friendly videos can be opened in Boxee’s in-app Web browser, which is still a relatively seamless experience.

It’s Like Instapaper For Video… Sort Of

To help bridge the gap between the desktop and the tablet, Boxee has a bookmarklet, which lets you send videos to Boxee from the browser. It’s a great feature, doing for video what Instapaper or Read It Later do for text. Of course, video formats and compatibility are not quite as universal as text; so, once again, this feature doesn’t work with all video content. We tried to add a video from The Daily Show‘s website to Boxee and watch it on the iPad, but were shown an error because the video was encoded with Flash.

To be fair, Boxee can’t be blamed for these limitations. Either The Daily Show and similar sites need to better encode their video content for iPads or, less realistically, Apple needs to change its uncompromising refusal to support Flash content on its mobile devices.

Like the “Friends” stream, the “Watch Later” feature works great with videos from YouTube, Vimeo and any other source that has non-Flash video content. And even if you end up saving a few Flash videos for later, you can always watch them on your desktop or television set, since the queue of content is synced with your Boxee account.

Stream Videos From Your Computer

In its most wholehearted attempt to circumvent the limitations of the iPad, the Boxee app lets you stream locally-stored video content wirelessly from your computer, which eliminates the need to convert that content into an iPad-friendly format. This process requires the Boxee Media Manager, an additional piece of software for the desktop, which lets you queue up local media files to be streamed to the iPad.