Hello - I'm new to the forums here and what an abundance of information and opinions on audio equip. Definately helped me out in narrowing things down.
So I guess I should start with what my thoughts were before jumping into the task. I JUST got the FJ last week today - love the car - wanted it to be my daily beater car cause it can take it. That being said - there were two things that needed IMMEDIATE attention: 1. Headlights / 2. Stereo
1 - Changed out the bulbs to PIAAs Super Whites - wanted straight white, the blue tints on the Xtreme bulbs are ... eh... not me - I've got HIDs in everything, but for the FJ - I'll stick the PIAAs for now. (please no flames on the use of HIDs here

This was more for the speaker side of things)
2 - So, anybody who's done some research on their factory speakers know well that the speakers are worthless (they are to me anyways)! and as my daily beater, I'm gonna be spending a good amount of time in it - I've gotta enjoy my commute.
Since I had just bought the car last week - I'm still crinching at the fact I've "bought" a car - the wallet was feeling pretty light. So I had a choice - either replace the head unit or replace the speakers - but for today, not both.
Went to my local shop - and with the fact that I'm keeping the HU stock (FJammer), got myself some components of OZ Audio 180CS. Warm sound and crisp. I listen to a lot of vocals, so I like full mids and crisp highs - but NOT where the highs end up sounding like screeches.
Wasn't an easy task to do, you'll probably want to leave it to the professionals, unless you're an audio veteran. Had a plate made to replace the 6x9 setup - to a 6.5; and a plate for the tweeters where the 3.5" dashes were.
The sounds are MUCH better. It sounds fuller and you can actually hear the sound from the dash too. You still know that the speakers are underpowered, but that can wait - the new speakers DEFINATELY make me a happier commuter.
I don't have any pics of installation - but everything does fit like stock - panels work to keep the "stock look."
Just wanted to be another one to confirm that speaker upgrades alone will make a difference. I usually don't haul people around - so replacing the rear speakers are not that high on my list - but "next" thing I'd probably look into would be the use of an amp - Gotta dig through my garage to see if I have any extras laying around.