For a long time I didn't use fan expansions because I couldn't think of a good way to properly integrate them into my collection.
Initially I was thinking of using some of the blank cards and writing a 1 on 12, a 2 on 12, etc. Then if we wanted to use a fan card we would just pull the number of stacks of blanks as needed to fill the spots (with appropriate number of cards for the stack [10/8/12]) and I'd have a print out of the card (probably 4 copies of each) that would be next to each person in number order for their reference during the game. The upside is that I wouldn't need to print nearly as many pages and would save a lot of space in my storage solution. The downside is that people will either need to memorize the fan cards or be looking at the reference when planning their next hand when they have one of the numbered cards in hand.
The alternative solution that I ended up going with was buying the second edition of base and intrigue, pulling out the new cards, then using all the duplicate cards as "backers" for printed fan cards; attaching the printed card to the dominion card with scrapbooking double sided tape (strong enough to prevent the printed paper from getting to the edge of a sleeve revealing that it's a fan card when next on the deck, but made to be non-damaging if ever removed). It does make the card a tiny bit thicker, but not enough to be noticeable in a deck stack. This does require printing off the full amount of cards, which ends up costing a bit and taking more storage space, but provides a more natural integration into the game.
Do any other people on this site use the fan expansions? How do you integrate them?