I will leave specific recommendations to others, but I favor http://www.jetpens.com/ for being able to easily buy singles of many different pens and notebooks and try them out for yourself.

Depends on what you want, as there's a lot of options. However, I will share the pens and paper of various kinds I like:

    pens:
        [0] Pilot Razer Point (Black, very fine point)
        [1] Uni-Ball Stick Micro Point (Blue, ball-point but with fluid ink)
        [2] BIC Cristal Ballpoint (Black, extremely cheap)

    Paper:
        [3] TOPS The Legal Pad (white, standard us size, wide ruled)
        [4] Staedtler Engineers Notepaper (lightly gridded)
        [5] Moleskine Notebooks (Large size, hardcover, gridlines)

[0] - http://www.amazon.com/Pilot-Razor-Point-Marker-Stick/dp/B000...

[1] - http://www.amazon.com/uni-ball-Stick-Micro-Roller-60151/dp/B...

[2] - http://www.amazon.com/BIC-Cristal-Ballpoint-Pen-Medium/dp/B0...

[3] - http://www.amazon.com/Legal-Inches-Perforated-White-Sheets/d...

[4] - http://www.amazon.com/Staedtler-Translucent-Bond-Pads-100/dp...

[5] - http://www.amazon.com/Moleskine-Classic-Notebook-Squared-Not...

Pens are very subjective, notebook paper is not. Thicker/heavier paper is almost always better. Moleskine paper is good, Rhodia paper (80gsm) is better, Clairefontaine paper (90gsm) is great. You can buy even heavier paper (67lb, 110lb, etc), but it usually doesn't come in notebooks.

Pens are all different: there are good gel pens (Sakura Gelly Roll, Pilot G2), good fountain pens (Lamy Safari, many many more), good art pens (Sakura Pigma Micron), good fine-point pens (Pentel Slicci, Uniball Signo Bit), and even good ballpoint pens (I like Skilcraft retractables, plus that 4-color Zebra pen). Some will bleed through on thin paper (especially fountain pens), so you lose 1/2 your notebook capacity. Not all pens/inks are waterproof (!).

Pilot G-Tec-C4 Rollerball Pen is affordable and well regarded with a practical narrow stroke. Have used these for many years. Silvine pocket notebooks are affordable and well made.

Pen: Jinhao X750 ($10) is a no-brainer. Or the Platinum Carbon desk pen ($12) if you like really thin lines.

Notebooks: Rhodia, Clairefontaine, Leuchtturm1917, or equivalent quality. Should be around $15 depending on size. Moleskines are no-go (ink bleeds through page)

Ink: Private Reserve is a nice starting point. I am particularly fond of their foam green. $11 for a 66ml bottle.

Shop: I really like Goulet Pens. Good service, amazingly careful packaging.

Source: personal experience and preference.

I've tried them all, Rapidograph technical pens, Pelican and Montblanc fountain pens, roller ball, gel pens, and ball points, and even space pens. Fountain pens feel nicest, but they are the most trouble. Very expensive ones can be beautiful and collectable, but once one reaches the price point where the nib is a quality nib the writing experience doesn't improve much. The best way to pick a fountain pen is to go to a store that specializes in fountain pens and actually test some out. Some feel too big, some too small, some the cap doesn't work the way I want, but the most important thing is the way the ink flows on the paper. My very best was a high end Scheaffer from almost 40 years ago, still much less expensive than a Montblanc. However, fountain pens don't suit me well because I often wear t-shirts these days and work in a variety of settings, and the need to refill and care for fountain pens make them less practical for me.

Gel pens tend to smear a bit too much for my taste and run out of ink more quickly than I'd like. The rollerball pens often feel a bit too scratchy on the paper.

Most traditional ball points of any quality retract their point by clicking. I find that this is great for carrying a pen around in one's pocket, but the ball point tip invariably has a slight amount of play since it is not attached to the pen but simply passes though an opening in the outer cylinder of the pen.

I notice this troublesome movement at the tip the most when doing complex mathematics. Once I'm working with small subscripts I want the pen's tip to start writing at precisely the location that I've placed it on the paper. For this reason I recommend a ball point with a cap where the tip is actually affixed in position and doesn't retract. The Pentel R.S.V.P line has pens like this and they work very well for me. The pen is comfortable to hold, having a wider barrel than many cheap pens and incorporates a elastomeric sleeve where one's fingers grip it. The barrel is a good length to it works well with or without the cap. The "fine" size make nice thin lines, the tip is of higher quality than many other ballpoints I've tried and doesn't skip for me at all, nor does it collect a little ball of gooey ink that will be deposited on the paper at the most inappropriate place.

In addition to being reasonably priced the Pentel R.S.V.P line can be found everywhere, Office Depot, college bookstores, and even the supermarket. The pens are also available in a range of colors, two line weights, and even variations like short ones (intended to be carried in a small pocket) or ones that click to retract the tip (but see my comments above).

My favorite ink color is purple. I generally got very good grades in grad school and I was thinking one day while fishing out my paper from a stack of graded papers that it would be easier to find if I turned in my homework on a off-white or pale yellow paper. I started doing this and then adopted the convention of doing my work and tests in purple ink as well. My thinking was that the overworked graders would learn that my work on homework and tests in purple ink was almost always correct, and I believed that sometimes I got the benefit of the doubt when they had to interpret a weaker answer of mine because of the purple ink. For business use I revert back to blue-black ink.

As for paper, I really like Japanese notebooks. The paper is of high quality, and I like the narrower aspect ratio of ISO notebooks because it fits easier into a backpack.

Pilot Precise V5 is the best pen for the money.