My favorite mod was swapping out the original cheesy 3 speed gear box, to a 5 speed. Really made the car fun and peppy.
The second was installing A/C.
I could have stopped right there, but got totally carried away.

 

If you are keeping it a 6, then split headers, dual exhaust, and a 2 bbl carb are some pretty worthwhile upgrades. Another pretty common (and cheap) upgrade is electronic ignition, which will be my next upgrade after I get a paint job. A power brake booster with a dual master cylinder would upgrade your braking to more modern safety standards, and help out a lot. I'll be doing this somewhere down the line, too. I've heard a lot of good things about a 5 speed, but I haven't really looked into it myself.

Some more upgrades that are pretty common and neat -

LED Taillights w/ Sequential Turn Signals (worth it!)
Halogen Headlights
Power Steering
Aftermarket Steering Wheel
Console
New Wheels/Wheel Covers
New Chrome/Paint/General Restoration Things
A New Stereo
Deluxe Interior Upgrade

Just remember, money is better spent on getting your car reliable and road worthy before hot rodding it with all the cool aftermarket parts. The best upgrades are the ones that make your car more driveable. I find myself wishing that I would have saved up for a paint job at this point rather than spent my money elsewhere, but that's beside the point. It'll all come eventually.

 

I agree with the comments relating to making it safe and reliable before upgrading alot.

The split manifold/header with 2 inch dual exhaust and a pair of Dynomax Superturbo mufflers would be cool. Don't go with big exhaust pipe. Also having the exhaust exit with turndowns at the rear valance looks sweet.

A 2bbl carb upgrade would be nice too, but if you stay with the 1bbl use the Autolite not the Holley.

Take a look here for I6 stuff.

http://www.fordsix.com/
http://www.classicinlines.com/

Something inexpensive you can do is get a pair of GE Nighthawk 1157 bulbs from Amazon for the tail lights. They are the same as the stock bulb but have a different filiment so they are a bit brighter especially on brake. I run them with my incandescant sequential tails.

Halogen headlights are a must for a car that is driven. I use Sylvania Xtravision 6024 and a pair of relays to run them.

 

I wouldn't buy all my parts from the parts suppliers for them either. Classic Inlines and Clifford are overpriced on everything they have. I put together my DSII kit for under $150, my header was under $300, and my carb setup was right around $100.

 

Do fuzzy dice count as a modification?

I did modern brakes, suspension, steering and motor. Drives like a dream.

 

BA is right, you can find better deals. Thats more for reference.