This approach is a little long winded, but it gets the desired result given what we've got to work with. I've only tried this with Vista Media Center, so am unsure if it works with any other media applications.
1. First of all set up your Freeview and Sky TV channels as per usual. If you aren't running Sky directly in VMC or don't have Sky, then just set up Freeview. I'll call these your 'watchable' channels.
2. Do a transponder scan on the following transponders (depending on what channels you require) to pick up the 'raw' (encoded) Sky channels. (note that this is a list of only the channels I have. If you subscribe to any other Sky channels, you'll need to find the appropriate transponders)
12421H - CI, CNBC, Fashion TV, Alt TV, Fox News, Documentary Channel
12519H - 63, Cartoon Network, Sky News
12546H - Food Television, History Channel, Living Channel, Playhouse, Sky Sport 1, Sky Sport H/L?s
12581H - BBC World, Nat Geographic, Sky Sport 2, UKTV, Vibe
12608H - Discovery, E!, Juice TV, Shine, Sky Sport 3, the BOX
12644H - C4, ESPN, Nickelodeon, TV 3
12671H - Trackside, TV 2, TV One
12707H - Animal Planet, CNN, Disney Channel, MTV, Prime
(For Alt TV, Documentary Channel, and Fox News, these channels actually appear after the scan for the Freeview channels. You'll see them in the channel list with a little padlock against them. Use these to set up your EPG as per below)
You will use these scrambled channels to update your EPG.
3. Now this is an important step. All of the new channels scanned in above will be allocated to the last numbers in your guide. Go through and edit the name of each and add something like EPG to the end. This is so you can distinguish the 'watchable' channels from the scrambled ones apart when you continue with the set up.
4. In Tasks>TV>Guide, select Edit Listings of one of the working channels in your list. From the list of channels presented, scroll down until you find the equivalent scrambled Sky channel (which should have something like EPG at the end of the name as set up in step 3). Click on that channel and select the option which merges the guide from that channel with your 'watchable' channel (the second option in the list).
5. Complete step 4 for all your 'watchable' channels.
6. Select one channel from each transponder (I use a channel which I hardly watch for reasons which will become more apparent in the next step), and rename it EPG1, EPG2 etc.
7. Go through the rest of the scrambled Sky channels and hide them from the VMC guide. Leave the ones you've renamed to EGP1, EPG2 etc visible in the guide, and give them the highest channel numbers. I've started mine from 501 and upwards. Because these channels are visible in your guide, you want them to be channels that you hardly ever watch so you don't try to watch them by mistake as they are scrambled and unwatchable.
8. Set up regular recordings for each of the EPG1, EPG2 etc channels you have. Each time they record, they will update the guide on all the channels for which they share the same responder. I've set mine up to record for 1 minute each in the middle of the night (using MANUAL record), and set the series to overwrite the last recording. I've found that if you watch one channel on a transponder, it updates the guide for ALL channels on that same transponder, even if you watch one of the scrambled channels. Recording that one channel does the same trick as watching it.
The drawbacks of this setup is that you have random unwatchable channels in your guide. But if you put them at the end of the guide, and use channels which you do not watch often, this limits any confusion. Also, you'll have X number of recorded programs which will always be there, which clutter up your recorded TV section somewhat. Thirdly, you'll have loads of extra scheduled recordings listed. Finally, you'll have a tuner conflict if you try to record a program at the same time the guide is updating. I got around this by recording to update the guide in the dead of the night.
The benefits are that your guide is always up to date, and that recording from your Freeview feed is 100% stable (ok, as close as VMC lets you get to being stable anyway).
Hopefully this guide makes sense. If there are parts which are hard to understand, please let me know and I'll reword accordingly.
I hope this helps someone else as much as it has helped me!
EDIT - I've updated the format of this post, a couple of key instructions, the list of transponders, and changed it to reflect the recent VMC update which removes the Freeview series recording issue.