I've never used an agency, I get scared that something will be wrong, or go wrong (insert control freak lit sign overhead here...)
This is what I've done for the past trips:
Room only reservation thru 1-407-939-7675. I've always gotten a 20%
AAA discount, but that might just be timing or luck. Usually $76/night at POP or ASMu. I take surveys online to help with costs, so I use a Disney Gift Card as my deposit, then as I get more cards I call and apply to my balance so the room is paid in full at check-in.
Tickets: Parkhoppers through mousesavers/undercovertourist. I can't say enough good things about them!
Food: We usually only have 2-3 TS just because I hate having to be somewhere at a specific time, but like them for Fantasmic or character meals. I use gift cards for these also. I pay cash or use Disney Dollars (also from surveys) to pay for CS meals and snacks. I'm opposite of most, I don't really like having everything on one card. I like things compartmentalized. I kind of know ahead what CS cost, so I keep that money/card separate, then I have one bigger amt card for just fun purchases. So when that card is used I'm done shopping!

Usually.
Flight: I fly with Spirit, so can usually get good deals, last trip Dec07 was $88 round trip per person. With this economy, I doubt I can beat that, but they usually have a decent sale if you hit them right, I'm on the email alert list.
I take one credit card for emergencies, but have never used one.
So far for my 2010 trip I have $450 paid on the room, $195 in disney dollars, and 3 $25 Landry's card for Rainforest Cafe/TRex/Yak&Yeti. These were all from surveys over the past year. I guess b/c of the oddball way I pay it is just easier for me to do it myself rather than a package or an agent.
My friend is just the opposite, she calls her agent gives dates and idea of what she wants and just sits back. I'd go insane! It all depends on what works best for you.