I use the online version, not the PDF, partly because it's more up-to-date, and partly because I'm often not at my home computer.
For a specific card, I look at the card entry and then do a global search on the card name to see where else it's mentioned (identifier lists, Special Conditions, etc). Since I used the online version, the search isn't very helpful - it does a search for ANY keywords, not ALL, and I don't think it did quoted phrases, so even a card like New Jerusalem would bring up every page with "new" and every page with "jerusalem" (most of which are not about New Jerusalem).
For a rule, I would rarely do a search unless I remembered some unique wording about it. Instead, I would read through the How to Use, Default Conditions, and Special Conditions for an ability type (the distinctions between the three sections rarely mattered, I would much rather one long page with all the info than three small pages each with some seemingly random portion of the info) for help. Occasionally I'd venture to the rulebook if I couldn't find it, and then at worst I'd do a global search. (The search results aren't always helpful, as so many of them are along the lines of "How to Use" without telling you the category. I'd like their titles to be something like "Capture > How to Use" for that.)
The glossary is helpful for identifiers, and they'd be even better if they were more up-to-date (musicians, etc.). I like that functionality as it is.
It's seemingly inconsistent what boxes are popped up and which redirect you to a new page. I middle-click as much as possible because of that, for some tab-splosion.
I would also like card entries for non-special ability cards - it's still nice to be able to click on Babylon and see it's a Red site from the "Babylonian sites" entry, or whatever, and see the card image and what identifiers it has (what exactly is Samuel?).
