Goodreader, I cannot recommend thee enough.
I've tried a few apps on my 3G, and since I'm usually reading large PDFs, the experience was lacking. The apps would occasionally crash, and browsing was slow. Until Goodreader. It renders one page at a time, so the whole thing isn't in memory. It does mean that there's a slight lag when turning pages (instead of the smooth-ish scrolling you get when it's all prerendered), but it's way better than crashing. It's not free, but it's the only PDF reader I'd recommend--and it's a bargain for the price.
Oh, and it downloads PDFs from the web quite easily, so I just checked out that transit schedule. Works fine. The schedule itself looks like it was made to be printed out to something like four pages wide for each page (so something like a 34 inch width), so reading the large-ish tables on the iPhone is not the most rewarding experience--but it renders and scrolls around and such just fine.
Seriously, check it out. It also supports rotation lock and wifi transfer; I haven't tested the latter since it's usually really easy to just snag a PDF from a given URL (which is then stored locally, on the phone).
