Ideally, beans should be planted in the final container, as they do not like being transplanted, either that, or you can plant them in peat pots and then when the seedlings are ready, plant the entire peat pot in the final spot [make sure the top rim is slightly (1/4 inch) below soil level, or it will wick away water from around the seedling], whereupon the peat pot will break down in the soil. When transplanting a bean seedling to its final spot, handle it very gently so as to disturb the roots as little as possible. Be sure to plant it at the same depth that it was in the pot (they are fussy). Squash has fragile roots, so when transplanting, be very gentle; ideally, like beans, they should be planted in their final site.
Most seedlings should be transplanted to individual containers when they grow their second or third set of true leaves. The first "leaves" to appear will be the cotyledons, which are not true leaves, and will often have a different shape that the true ones.
If your plants are already outdoors, then you don't need to worry about hardening off. [If they are indoors, you'd need to gradually introduce them to outdoor conditions, by placing them in a shaded, protected area for a few hours each day, increasing the amount of time each successive day-take them in at night. After about 7 to 10 days, they should be ready to plant outdoors.]
Tomatoes usually emerge within 5 to 10 days, it could be that your other seeds may germinate soon; cooler soil temperatures may delay germination. Make sure the soil is at optimum temperature, and don't over- or underwater. Also, the older the seed is, the less will sprout. Transplant tomato seedlings the first time to individual pots when they have their second pair of true leaves (about 3 to 4 inches tall); transplant to the final spot when they are about 6 to 10 inches tall, after they have developed a healthy root system and a good set of leaves.