I'm a big fan of Taqueria Los Primos at the intersection of Newport Gap Pike and Old Capitol Trail (behind Price's Corner). $2.25 and you literally watch them make your damn tortilla right in front of you and toss it on the griddle. Be prepared to speak rudimentary spanish when placing your order - bistek = beef, pastor = pork, chorizo (obvious), and the place is so tipico that they have tripe and tongue too. Their menudo is probably pretty amazing but they are always sold out when I go!
Taqueria Los Primos
3322 Old Capitol Trl, Wilmington, DE 19808
My favorite holes in the wall are Mexican, specifically tacos. There is a whole thread on CH from years ago that explored Wilmington's taco options: http://chowhound.chow.com/topics/356888
Kahl-Bee Korean *used* to be a hole in the wall, but isn't one any more. It's still good though.
I am also fond of some of the BBQ holes in the wall, although some people disagree with me on those. Sunset Grill on Rte 9 in New Castle is my favorite close to home.
Kahl-Bee Korean Restaurant
2011 Kirkwood Hwy, Wilmington, DE 19805
I'm a fan of Alpha Pizza on Rt 4 in Newport. It's a family run pizza place- no delivery, no menus, but you can use the drive thru window from when it was a Wendy's years ago. Their pizza is a Greek style pizza (saucy, thick crust), and they have a killer stromboli. Their breakfast sandwiches are no joke either. Their sausage has to be fresh or just a really good brand because it's delicious.
1402 E Newport Pike, Wilmington, DE 19804